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@@ -1149,7 +1149,7 @@ <h3 class="callout-title">Challenge</h3>
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 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Setting the Random Seed </h3>
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 <p>Whenever your code involves the generation of random numbers, it’s a
 good practice to set the random seed in R with
@@ -1457,7 +1457,7 @@ <h3 class="callout-title">Challenge</h3>
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 <p>You set <code>nmads = 4</code> like so:</p>
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   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
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 <p><code>modelGeneVar()</code> can take a <code>block</code>
 argument.</p>
@@ -1862,7 +1862,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
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 <p>Use the <code>block</code> argument in the call to
 <code>modelGeneVar()</code> like so:</p>
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   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
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 <p>The first few lines here read the data from ExperimentHub and the
 mitochondrial genes are identified by gene symbols in the row data.
@@ -2416,7 +2416,7 @@ <h3 class="callout-title">Extension challenge 1: Spike-ins</h3>
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 <p>Spike-ins are deliberately-introduced exogeneous RNA from an exotic
 or synthetic source at a known concentration. This provides a known
@@ -2460,7 +2460,7 @@ <h3 class="callout-title">Extension challenge 3: Reduced dimensionality represen
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 <p>Mathematically, this would require the data to fall on a
 two-dimensional plane (for linear methods like PCA) or a smooth 2D
@@ -2734,7 +2734,7 @@ <h3 class="callout-title">Challenge</h3>
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 <p>We see in the help documentation for <code>?clusterCells</code> that
 all of the clustering algorithm details are handled through the
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 <p>You can see that at least among the top markers, cluster 6 (pale
 green) tends to have the least separation from cluster 1.</p>
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 <p>The <code>NNGraphParam</code> constructor has an argument
 <code>cluster.args</code>. This allows to specify arguments passed on to
@@ -3660,7 +3660,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
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 <p>One important reason why is because averages over all other clusters
 can be sensitive to the cell type composition. If a rare cell type shows
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 <p>Use <code>BiocParallel</code> and the <code>BPPARAM</code> argument!
 This example will set it to use four cores on your laptop, but you can
@@ -3848,7 +3848,7 @@ <h3 class="callout-title">Extension Challenge 3: Critical inspection of diagnost
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 <p>The example that jumps out most strongly to the eye is ExE endoderm,
 which doesn’t show clear separate modes. Simultaneously, Endothelium
@@ -4141,7 +4141,7 @@ <h3 class="callout-title">Challenge</h3>
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 <p>Samples 5 and 6 were from the same “pool” of cells. Looking at the
 documentation for the dataset under <code>?WTChimeraData</code> we see
@@ -4206,7 +4206,7 @@ <h3 class="callout-title">Challenge</h3>
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 <p>False. Batch-level data can be retained through confounding with
 experimental factors or poor ability to distinguish experimental effects
@@ -4659,7 +4659,7 @@ <h3 class="callout-title">Challenge</h3>
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 <p>“logFC” stands for log fold-change. <code>edgeR</code> uses a log2
 convention. Rather than reporting e.g. a 5-fold increase, it’s better to
@@ -4985,7 +4985,7 @@ <h3 class="callout-title">Exercise 1: Heatmaps</h3>
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 <p>You can simply hand <code>pheatmap()</code> a matrix as its only
 argument. <code>pheatmap()</code> has a million options you can tweak,
@@ -4999,7 +4999,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
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 <p>After running the second pseudobulk DGE, you can join the two
 <code>DataFrame</code>s of <code>Erythroid3</code> statistics using the
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 </button>
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@@ -5132,7 +5132,7 @@ <h3 class="callout-title">Extension challenge 1: Group effects</h3>
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 <p>It’s important to have multiple samples within each experimental
 group because it helps the batch effect correction algorithm distinguish
@@ -5209,7 +5209,7 @@ <h3 class="callout-title">Key Points</h3>
  -->
 </section></section><section id="aio-large_data"><p>Content from <a href="large_data.html">Working with large data</a></p>
 <hr>
-<p>Last updated on 2024-10-02 |
+<p>Last updated on 2024-10-04 |
 
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/large_data.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
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 <p>From <code>?MulticoreParam</code> :</p>
 <blockquote>
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 <pre class="output" tabindex="0"><code>     approx
-exact   1   2   3   4   5   6   7   8   9  10  11  12  13  14
-   1   90   0   0   0   0   0   0   0   1   0   0   0   0   0
-   2    0 143   0   1   0   0   0   0   0   0   0   0   0   0
-   3    0   0  77   0   0   0   0   0   0   0   0   0   0   0
-   4    0   0   0 397   0   0   0   0   0   0   0   0   0   0
-   5    0   0   0   0 393   0   0   2   0   0   0   5   0   0
-   6    0   0   0   0   0 204   6   0   0   0   1   0   0   0
-   7    0   0   0   0   0   0 245   0   0   1   0   0   0   0
-   8    0   0   0   0   1   0   0  93   0   0   0   0   0   0
-   9    1   0   0   0   1   0   0   0 106   0   0   0   0   0
-   10   0   0   0   0   0   0   0   0   0 116   2   1   0   0
-   11   0   0   0   0   0   0   0   0   0   2 139   0   6   0
-   12   0   0   0   0   1   0   0   0   0   0   0 210   0   0
-   13   0   0   0   0   0   0   0   0   0   0   0   0 146   0
-   14   0   0   0   0   0   0   0   0   0   0   0   0   0  20</code></pre>
+exact   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15
+   1   88   0   0   0   0   0   0   2   0   0   0   1   0   0   0
+   2    0 143   0   1   0   0   0   0   0   0   0   0   0   0   0
+   3    0   0  75   0   0   0   0   0   0   0   0   2   0   0   0
+   4    0   0   0 198   0   0   0   0   0   0   0   0 143   0   0
+   5    0   0   0   0  71   0   0   0   1   0   3 322   0   0   0
+   6    0   0   0   0   0 210   0   0   0   0   0   0   0   0   0
+   7    0   0   0   0   0   0 245   0   1   0   0   0   0   0   0
+   8    0   0   0   0  95   0   0   0   0   0   0   0   0   0   0
+   9    1   0   0   0   0   0   0 106   0   0   0   1   0   0   0
+   10   0   0   0   0   0   0   0   0 112   0  10   0   0   0   0
+   11   0   0   0   0   0   0   0   0   0 153   0   0   0   0   0
+   12   0   0   0   0   8   0   0   0   0   0 195   1   0   0   0
+   13   0   0   0   0   0   0   0   0   1   0   0   0   0 146   0
+   14   0   0   0   0   0   0   0   0   0   0   0   0   0   0  20
+   15   0   0   0  56   0   0   0   0   0   0   0   0   0   0   0</code></pre>
 </div>
 <p>The similarity of the two clusterings can be quantified by
 calculating the pairwise Rand index:</p>
@@ -5845,12 +5846,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="callout-inner">
 <h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
-<p>The uncertainty from approximation error is sometimes psychologically
-objectionable. “Why can’t my computer just give me the right answer?”
-One way to alleviate this feeling is to quantify the approximation error
-on a small test set like the sce we have here. Using the
-<code>ExactParam()</code> class, visualize the error in PC1 coordinates
-compared to the RSVD results.</p>
+<p>The uncertainty from approximation error is sometimes aggravating.
+“Why can’t my computer just give me the right answer?” One way to
+alleviate this feeling is to quantify the approximation error on a small
+test set like the sce we have here. Using the <code>ExactParam()</code>
+class, visualize the error in PC1 coordinates compared to the RSVD
+results.</p>
 </div>
 </div>
 </div>
@@ -5859,7 +5860,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>This code block calculates the exact PCA coordinates. Another thing
 to note: PC vectors are only identified up to a sign flip. We can see
@@ -6270,7 +6271,7 @@ <h3 class="callout-title">Exercise 1: Out of memory representation</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>See the <code>HDF5Array</code> function for reading from HDF5 and the
 <code>writeHDF5Array</code> function for writing to HDF5 from the <em><a href="https://bioconductor.org/packages/3.19/HDF5Array" class="external-link">HDF5Array</a></em>
@@ -6284,7 +6285,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb50">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6292,61 +6293,52 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">wt_out</span> <span class="op">&lt;-</span> <span class="fu">tempfile</span><span class="op">(</span>fileext <span class="op">=</span> <span class="st">".h5"</span><span class="op">)</span></span>
 <span></span>
-<span><span class="va">wt_counts</span> <span class="op">&lt;-</span> <span class="fu">counts</span><span class="op">(</span><span class="fu">WTChimeraData</span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></code></pre>
-</div>
-<div class="codewrapper">
-<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="error" tabindex="0"><code>Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'counts': failed to load resource
-  name: EH2973
-  title: WT chimera processed counts (sample 9)
-  reason: 1 resources failed to download</code></pre>
-</div>
-<div class="codewrapper sourceCode" id="cb52">
-<h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu">writeHDF5Array</span><span class="op">(</span><span class="va">wt_counts</span>,</span>
+<span><span class="va">wt_counts</span> <span class="op">&lt;-</span> <span class="fu">counts</span><span class="op">(</span><span class="fu">WTChimeraData</span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">writeHDF5Array</span><span class="op">(</span><span class="va">wt_counts</span>,</span>
 <span>               name <span class="op">=</span> <span class="st">"wt_counts"</span>,</span>
 <span>               file <span class="op">=</span> <span class="va">wt_out</span><span class="op">)</span></span></code></pre>
 </div>
 <div class="codewrapper">
-<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="error" tabindex="0"><code>Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'is_sparse': object 'wt_counts' not found</code></pre>
-</div>
-<div class="codewrapper sourceCode" id="cb54">
-<h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">oom_wt</span> <span class="op">&lt;-</span> <span class="fu">HDF5Array</span><span class="op">(</span><span class="va">wt_out</span>, <span class="st">"wt_counts"</span><span class="op">)</span></span></code></pre>
-</div>
-<div class="codewrapper">
-<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="error" tabindex="0"><code>Error in file_path_as_absolute(path): file '/tmp/Rtmp6Q9gmL/file1e892f562866.h5' does not exist</code></pre>
+<pre class="output" tabindex="0"><code>&lt;29453 x 30703&gt; sparse HDF5Matrix object of type "double":
+                       cell_1     cell_2     cell_3 ... cell_30702 cell_30703
+ENSMUSG00000051951          0          0          0   .          0          0
+ENSMUSG00000089699          0          0          0   .          0          0
+ENSMUSG00000102343          0          0          0   .          0          0
+ENSMUSG00000025900          0          0          0   .          0          0
+ENSMUSG00000025902          0          0          0   .          0          0
+               ...          .          .          .   .          .          .
+ENSMUSG00000095041          0          1          2   .          0          0
+ENSMUSG00000063897          0          0          0   .          0          0
+ENSMUSG00000096730          0          0          0   .          0          0
+ENSMUSG00000095742          0          0          0   .          0          0
+         tomato-td          1          0          1   .          0          0</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb56">
+<div class="codewrapper sourceCode" id="cb52">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu">object.size</span><span class="op">(</span><span class="va">wt_counts</span><span class="op">)</span></span></code></pre>
+<code class="sourceCode R"><span><span class="va">oom_wt</span> <span class="op">&lt;-</span> <span class="fu">HDF5Array</span><span class="op">(</span><span class="va">wt_out</span>, <span class="st">"wt_counts"</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">object.size</span><span class="op">(</span><span class="va">wt_counts</span><span class="op">)</span></span></code></pre>
 </div>
 <div class="codewrapper">
-<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="error" tabindex="0"><code>Error in eval(expr, envir, enclos): object 'wt_counts' not found</code></pre>
+<pre class="output" tabindex="0"><code>1520366960 bytes</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb58">
+<div class="codewrapper sourceCode" id="cb54">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu">object.size</span><span class="op">(</span><span class="va">oom_wt</span><span class="op">)</span></span></code></pre>
 </div>
 <div class="codewrapper">
-<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="error" tabindex="0"><code>Error in eval(expr, envir, enclos): object 'oom_wt' not found</code></pre>
+<pre class="output" tabindex="0"><code>2488 bytes</code></pre>
 </div>
 </div>
 </div>
@@ -6372,7 +6364,7 @@ <h3 class="callout-title">Exercise 2: Parallelization</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
 <div class="accordion-body">
 <p>Use the function <code>system.time</code> to obtain the runtime of
 each job.</p>
@@ -6385,9 +6377,9 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb60">
+<div class="codewrapper sourceCode" id="cb56">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
diff --git a/cell_type_annotation.html b/cell_type_annotation.html
index c1aedd0..7d15de7 100644
--- a/cell_type_annotation.html
+++ b/cell_type_annotation.html
@@ -516,7 +516,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>We see in the help documentation for <code>?clusterCells</code> that
 all of the clustering algorithm details are handled through the
@@ -710,7 +710,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>You can see that at least among the top markers, cluster 6 (pale
 green) tends to have the least separation from cluster 1.</p>
@@ -1005,7 +1005,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb31">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1268,7 +1268,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb43">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1413,7 +1413,7 @@ <h3 class="callout-title">Exercise 1: Clustering</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>The <code>NNGraphParam</code> constructor has an argument
 <code>cluster.args</code>. This allows to specify arguments passed on to
@@ -1430,7 +1430,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb46">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1468,7 +1468,7 @@ <h3 class="callout-title">Exercise 2: Reference marker genes</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb47">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1541,7 +1541,7 @@ <h3 class="callout-title">Extension Challenge 1: Group pair comparisons</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
   <h4 class="accordion-header" id="headingSolution7"> Show me the solution </h4>
 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
+<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
 <div class="accordion-body">
 <p>One important reason why is because averages over all other clusters
 can be sensitive to the cell type composition. If a rare cell type shows
@@ -1575,7 +1575,7 @@ <h3 class="callout-title">Extension Challenge 2: Parallelizing SingleR</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
   <h4 class="accordion-header" id="headingSolution8"> Show me the solution </h4>
 </button>
-<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
+<div id="collapseSolution8" class="accordion-collapse collapse" aria-labelledby="headingSolution8" data-bs-parent="#accordionSolution8">
 <div class="accordion-body">
 <p>Use <code>BiocParallel</code> and the <code>BPPARAM</code> argument!
 This example will set it to use four cores on your laptop, but you can
@@ -1617,7 +1617,7 @@ <h3 class="callout-title">Extension Challenge 3: Critical inspection of diagnost
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
   <h4 class="accordion-header" id="headingSolution9"> Show me the solution </h4>
 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" data-bs-parent="#accordionSolution9" aria-labelledby="headingSolution9">
+<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
 <div class="accordion-body">
 <p>The example that jumps out most strongly to the eye is ExE endoderm,
 which doesn’t show clear separate modes. Simultaneously, Endothelium
diff --git a/eda_qc.html b/eda_qc.html
index a378a95..6615786 100644
--- a/eda_qc.html
+++ b/eda_qc.html
@@ -497,7 +497,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb4">
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@@ -578,7 +578,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Setting the Random Seed </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <p>Whenever your code involves the generation of random numbers, it’s a
 good practice to set the random seed in R with
@@ -797,7 +797,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>You set <code>nmads = 4</code> like so:</p>
 <div class="codewrapper sourceCode" id="cb24">
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   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb42">
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@@ -1181,7 +1181,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p><code>modelGeneVar()</code> can take a <code>block</code>
 argument.</p>
@@ -1194,7 +1194,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <p>Use the <code>block</code> argument in the call to
 <code>modelGeneVar()</code> like so:</p>
@@ -1405,7 +1405,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb56">
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@@ -1569,7 +1569,7 @@ <h3 class="callout-title">Exercise 1: Normalization</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb66">
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@@ -1628,7 +1628,7 @@ <h3 class="callout-title">Exercise 2: PBMC Data</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
   <h4 class="accordion-header" id="headingSolution7"> Show me the solution </h4>
 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
+<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
 <div class="accordion-body">
 <p>The first few lines here read the data from ExperimentHub and the
 mitochondrial genes are identified by gene symbols in the row data.
@@ -1736,7 +1736,7 @@ <h3 class="callout-title">Extension challenge 1: Spike-ins</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
   <h4 class="accordion-header" id="headingSolution8"> Show me the solution </h4>
 </button>
-<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
+<div id="collapseSolution8" class="accordion-collapse collapse" aria-labelledby="headingSolution8" data-bs-parent="#accordionSolution8">
 <div class="accordion-body">
 <p>Spike-ins are deliberately-introduced exogeneous RNA from an exotic
 or synthetic source at a known concentration. This provides a known
@@ -1780,7 +1780,7 @@ <h3 class="callout-title">Extension challenge 3: Reduced dimensionality represen
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
   <h4 class="accordion-header" id="headingSolution9"> Show me the solution </h4>
 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" data-bs-parent="#accordionSolution9" aria-labelledby="headingSolution9">
+<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
 <div class="accordion-body">
 <p>Mathematically, this would require the data to fall on a
 two-dimensional plane (for linear methods like PCA) or a smooth 2D
diff --git a/index.html b/index.html
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--- a/index.html
+++ b/index.html
@@ -372,7 +372,7 @@ <h4 class="accordion-header" id="headingSolution1">
   If you already have R and RStudio installed
   </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <ul><li>Open RStudio, and click on “Help” &gt; “Check for updates”. If a new
 version is available, quit RStudio, and download the latest version for
@@ -398,7 +398,7 @@ <h4 class="accordion-header" id="headingSolution2">
   If you don’t have R and RStudio installed
   </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <ul><li>Download R from the <a href="https://cran.r-project.org/bin/windows/base/release.htm" class="external-link">CRAN
 website</a>.</li>
@@ -429,7 +429,7 @@ <h4 class="accordion-header" id="headingSolution3">
   If you already have R and RStudio installed
   </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <ul><li>Open RStudio, and click on “Help” &gt; “Check for updates”. If a new
 version is available, quit RStudio, and download the latest version for
@@ -453,7 +453,7 @@ <h4 class="accordion-header" id="headingSolution4">
   If you don’t have R and RStudio installed
   </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <ul><li>Download R from the <a href="https://cran.r-project.org/bin/macosx/" class="external-link">CRAN website</a>.</li>
 <li>Select the <code>.pkg</code> file for the latest R version</li>
@@ -486,7 +486,7 @@ <h4 class="accordion-header" id="headingSolution5">
   Install R using your package manager and RStudio
   </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
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 <div class="accordion-body">
 <ul><li>Follow the instructions for your distribution from <a href="https://cloud.r-project.org/bin/linux" class="external-link">CRAN</a>, they provide
 information to get the most recent version of R for common
diff --git a/instructor/aio.html b/instructor/aio.html
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@@ -1153,7 +1153,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb4">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1235,7 +1235,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Setting the Random Seed </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <p>Whenever your code involves the generation of random numbers, it’s a
 good practice to set the random seed in R with
@@ -1461,7 +1461,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>You set <code>nmads = 4</code> like so:</p>
 <div class="codewrapper sourceCode" id="cb24">
@@ -1737,7 +1737,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
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   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
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 <div class="codewrapper sourceCode" id="cb42">
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 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p><code>modelGeneVar()</code> can take a <code>block</code>
 argument.</p>
@@ -1866,7 +1866,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <p>Use the <code>block</code> argument in the call to
 <code>modelGeneVar()</code> like so:</p>
@@ -2082,7 +2082,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
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 <div class="codewrapper sourceCode" id="cb56">
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@@ -2253,7 +2253,7 @@ <h3 class="callout-title">Exercise 1: Normalization</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
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 <div class="codewrapper sourceCode" id="cb66">
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@@ -2312,7 +2312,7 @@ <h3 class="callout-title">Exercise 2: PBMC Data</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
   <h4 class="accordion-header" id="headingSolution7"> Show me the solution </h4>
 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
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 <div class="accordion-body">
 <p>The first few lines here read the data from ExperimentHub and the
 mitochondrial genes are identified by gene symbols in the row data.
@@ -2420,7 +2420,7 @@ <h3 class="callout-title">Extension challenge 1: Spike-ins</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
   <h4 class="accordion-header" id="headingSolution8"> Show me the solution </h4>
 </button>
-<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
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 <div class="accordion-body">
 <p>Spike-ins are deliberately-introduced exogeneous RNA from an exotic
 or synthetic source at a known concentration. This provides a known
@@ -2464,7 +2464,7 @@ <h3 class="callout-title">Extension challenge 3: Reduced dimensionality represen
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
   <h4 class="accordion-header" id="headingSolution9"> Show me the solution </h4>
 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" data-bs-parent="#accordionSolution9" aria-labelledby="headingSolution9">
+<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
 <div class="accordion-body">
 <p>Mathematically, this would require the data to fall on a
 two-dimensional plane (for linear methods like PCA) or a smooth 2D
@@ -2739,7 +2739,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
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 <div class="accordion-body">
 <p>We see in the help documentation for <code>?clusterCells</code> that
 all of the clustering algorithm details are handled through the
@@ -2936,7 +2936,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
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 <p>You can see that at least among the top markers, cluster 6 (pale
 green) tends to have the least separation from cluster 1.</p>
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 </button>
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 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
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@@ -3648,7 +3648,7 @@ <h3 class="callout-title">Exercise 1: Clustering</h3>
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   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
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 <p>The <code>NNGraphParam</code> constructor has an argument
 <code>cluster.args</code>. This allows to specify arguments passed on to
@@ -3665,7 +3665,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
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   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
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@@ -3704,7 +3704,7 @@ <h3 class="callout-title">Exercise 2: Reference marker genes</h3>
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   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb47">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -3777,7 +3777,7 @@ <h3 class="callout-title">Extension Challenge 1: Group pair comparisons</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
   <h4 class="accordion-header" id="headingSolution7"> Show me the solution </h4>
 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
+<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
 <div class="accordion-body">
 <p>One important reason why is because averages over all other clusters
 can be sensitive to the cell type composition. If a rare cell type shows
@@ -3811,7 +3811,7 @@ <h3 class="callout-title">Extension Challenge 2: Parallelizing SingleR</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
   <h4 class="accordion-header" id="headingSolution8"> Show me the solution </h4>
 </button>
-<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
+<div id="collapseSolution8" class="accordion-collapse collapse" aria-labelledby="headingSolution8" data-bs-parent="#accordionSolution8">
 <div class="accordion-body">
 <p>Use <code>BiocParallel</code> and the <code>BPPARAM</code> argument!
 This example will set it to use four cores on your laptop, but you can
@@ -3853,7 +3853,7 @@ <h3 class="callout-title">Extension Challenge 3: Critical inspection of diagnost
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
   <h4 class="accordion-header" id="headingSolution9"> Show me the solution </h4>
 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" data-bs-parent="#accordionSolution9" aria-labelledby="headingSolution9">
+<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
 <div class="accordion-body">
 <p>The example that jumps out most strongly to the eye is ExE endoderm,
 which doesn’t show clear separate modes. Simultaneously, Endothelium
@@ -4147,7 +4147,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Samples 5 and 6 were from the same “pool” of cells. Looking at the
 documentation for the dataset under <code>?WTChimeraData</code> we see
@@ -4212,7 +4212,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>False. Batch-level data can be retained through confounding with
 experimental factors or poor ability to distinguish experimental effects
@@ -4665,7 +4665,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>“logFC” stands for log fold-change. <code>edgeR</code> uses a log2
 convention. Rather than reporting e.g. a 5-fold increase, it’s better to
@@ -4991,7 +4991,7 @@ <h3 class="callout-title">Exercise 1: Heatmaps</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>You can simply hand <code>pheatmap()</code> a matrix as its only
 argument. <code>pheatmap()</code> has a million options you can tweak,
@@ -5005,7 +5005,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb52">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -5040,7 +5040,7 @@ <h3 class="callout-title">Exercise 2: Model specification and comparison</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
 <div class="accordion-body">
 <p>After running the second pseudobulk DGE, you can join the two
 <code>DataFrame</code>s of <code>Erythroid3</code> statistics using the
@@ -5055,7 +5055,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb53">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -5138,7 +5138,7 @@ <h3 class="callout-title">Extension challenge 1: Group effects</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
 <div class="accordion-body">
 <p>It’s important to have multiple samples within each experimental
 group because it helps the batch effect correction algorithm distinguish
@@ -5215,7 +5215,7 @@ <h3 class="callout-title">Key Points</h3>
  -->
 </section></section><section id="aio-large_data"><p>Content from <a href="large_data.html">Working with large data</a></p>
 <hr>
-<p>Last updated on 2024-10-02 |
+<p>Last updated on 2024-10-04 |
 
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/large_data.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 12 minutes</p>
@@ -5634,7 +5634,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>From <code>?MulticoreParam</code> :</p>
 <blockquote>
@@ -5707,21 +5707,22 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="output" tabindex="0"><code>     approx
-exact   1   2   3   4   5   6   7   8   9  10  11  12  13  14
-   1   90   0   0   0   0   0   0   0   1   0   0   0   0   0
-   2    0 143   0   1   0   0   0   0   0   0   0   0   0   0
-   3    0   0  77   0   0   0   0   0   0   0   0   0   0   0
-   4    0   0   0 397   0   0   0   0   0   0   0   0   0   0
-   5    0   0   0   0 393   0   0   2   0   0   0   5   0   0
-   6    0   0   0   0   0 204   6   0   0   0   1   0   0   0
-   7    0   0   0   0   0   0 245   0   0   1   0   0   0   0
-   8    0   0   0   0   1   0   0  93   0   0   0   0   0   0
-   9    1   0   0   0   1   0   0   0 106   0   0   0   0   0
-   10   0   0   0   0   0   0   0   0   0 116   2   1   0   0
-   11   0   0   0   0   0   0   0   0   0   2 139   0   6   0
-   12   0   0   0   0   1   0   0   0   0   0   0 210   0   0
-   13   0   0   0   0   0   0   0   0   0   0   0   0 146   0
-   14   0   0   0   0   0   0   0   0   0   0   0   0   0  20</code></pre>
+exact   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15
+   1   88   0   0   0   0   0   0   2   0   0   0   1   0   0   0
+   2    0 143   0   1   0   0   0   0   0   0   0   0   0   0   0
+   3    0   0  75   0   0   0   0   0   0   0   0   2   0   0   0
+   4    0   0   0 198   0   0   0   0   0   0   0   0 143   0   0
+   5    0   0   0   0  71   0   0   0   1   0   3 322   0   0   0
+   6    0   0   0   0   0 210   0   0   0   0   0   0   0   0   0
+   7    0   0   0   0   0   0 245   0   1   0   0   0   0   0   0
+   8    0   0   0   0  95   0   0   0   0   0   0   0   0   0   0
+   9    1   0   0   0   0   0   0 106   0   0   0   1   0   0   0
+   10   0   0   0   0   0   0   0   0 112   0  10   0   0   0   0
+   11   0   0   0   0   0   0   0   0   0 153   0   0   0   0   0
+   12   0   0   0   0   8   0   0   0   0   0 195   1   0   0   0
+   13   0   0   0   0   0   0   0   0   1   0   0   0   0 146   0
+   14   0   0   0   0   0   0   0   0   0   0   0   0   0   0  20
+   15   0   0   0  56   0   0   0   0   0   0   0   0   0   0   0</code></pre>
 </div>
 <p>The similarity of the two clusterings can be quantified by
 calculating the pairwise Rand index:</p>
@@ -5852,12 +5853,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="callout-inner">
 <h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
-<p>The uncertainty from approximation error is sometimes psychologically
-objectionable. “Why can’t my computer just give me the right answer?”
-One way to alleviate this feeling is to quantify the approximation error
-on a small test set like the sce we have here. Using the
-<code>ExactParam()</code> class, visualize the error in PC1 coordinates
-compared to the RSVD results.</p>
+<p>The uncertainty from approximation error is sometimes aggravating.
+“Why can’t my computer just give me the right answer?” One way to
+alleviate this feeling is to quantify the approximation error on a small
+test set like the sce we have here. Using the <code>ExactParam()</code>
+class, visualize the error in PC1 coordinates compared to the RSVD
+results.</p>
 </div>
 </div>
 </div>
@@ -5866,7 +5867,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>This code block calculates the exact PCA coordinates. Another thing
 to note: PC vectors are only identified up to a sign flip. We can see
@@ -6277,7 +6278,7 @@ <h3 class="callout-title">Exercise 1: Out of memory representation</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>See the <code>HDF5Array</code> function for reading from HDF5 and the
 <code>writeHDF5Array</code> function for writing to HDF5 from the <em><a href="https://bioconductor.org/packages/3.19/HDF5Array" class="external-link">HDF5Array</a></em>
@@ -6291,7 +6292,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb50">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6299,61 +6300,52 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">wt_out</span> <span class="op">&lt;-</span> <span class="fu">tempfile</span><span class="op">(</span>fileext <span class="op">=</span> <span class="st">".h5"</span><span class="op">)</span></span>
 <span></span>
-<span><span class="va">wt_counts</span> <span class="op">&lt;-</span> <span class="fu">counts</span><span class="op">(</span><span class="fu">WTChimeraData</span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></code></pre>
-</div>
-<div class="codewrapper">
-<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="error" tabindex="0"><code>Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'counts': failed to load resource
-  name: EH2973
-  title: WT chimera processed counts (sample 9)
-  reason: 1 resources failed to download</code></pre>
-</div>
-<div class="codewrapper sourceCode" id="cb52">
-<h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu">writeHDF5Array</span><span class="op">(</span><span class="va">wt_counts</span>,</span>
+<span><span class="va">wt_counts</span> <span class="op">&lt;-</span> <span class="fu">counts</span><span class="op">(</span><span class="fu">WTChimeraData</span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">writeHDF5Array</span><span class="op">(</span><span class="va">wt_counts</span>,</span>
 <span>               name <span class="op">=</span> <span class="st">"wt_counts"</span>,</span>
 <span>               file <span class="op">=</span> <span class="va">wt_out</span><span class="op">)</span></span></code></pre>
 </div>
 <div class="codewrapper">
-<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="error" tabindex="0"><code>Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'is_sparse': object 'wt_counts' not found</code></pre>
-</div>
-<div class="codewrapper sourceCode" id="cb54">
-<h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">oom_wt</span> <span class="op">&lt;-</span> <span class="fu">HDF5Array</span><span class="op">(</span><span class="va">wt_out</span>, <span class="st">"wt_counts"</span><span class="op">)</span></span></code></pre>
-</div>
-<div class="codewrapper">
-<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="error" tabindex="0"><code>Error in file_path_as_absolute(path): file '/tmp/Rtmp6Q9gmL/file1e892f562866.h5' does not exist</code></pre>
+<pre class="output" tabindex="0"><code>&lt;29453 x 30703&gt; sparse HDF5Matrix object of type "double":
+                       cell_1     cell_2     cell_3 ... cell_30702 cell_30703
+ENSMUSG00000051951          0          0          0   .          0          0
+ENSMUSG00000089699          0          0          0   .          0          0
+ENSMUSG00000102343          0          0          0   .          0          0
+ENSMUSG00000025900          0          0          0   .          0          0
+ENSMUSG00000025902          0          0          0   .          0          0
+               ...          .          .          .   .          .          .
+ENSMUSG00000095041          0          1          2   .          0          0
+ENSMUSG00000063897          0          0          0   .          0          0
+ENSMUSG00000096730          0          0          0   .          0          0
+ENSMUSG00000095742          0          0          0   .          0          0
+         tomato-td          1          0          1   .          0          0</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb56">
+<div class="codewrapper sourceCode" id="cb52">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu">object.size</span><span class="op">(</span><span class="va">wt_counts</span><span class="op">)</span></span></code></pre>
+<code class="sourceCode R"><span><span class="va">oom_wt</span> <span class="op">&lt;-</span> <span class="fu">HDF5Array</span><span class="op">(</span><span class="va">wt_out</span>, <span class="st">"wt_counts"</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">object.size</span><span class="op">(</span><span class="va">wt_counts</span><span class="op">)</span></span></code></pre>
 </div>
 <div class="codewrapper">
-<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="error" tabindex="0"><code>Error in eval(expr, envir, enclos): object 'wt_counts' not found</code></pre>
+<pre class="output" tabindex="0"><code>1520366960 bytes</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb58">
+<div class="codewrapper sourceCode" id="cb54">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu">object.size</span><span class="op">(</span><span class="va">oom_wt</span><span class="op">)</span></span></code></pre>
 </div>
 <div class="codewrapper">
-<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="error" tabindex="0"><code>Error in eval(expr, envir, enclos): object 'oom_wt' not found</code></pre>
+<pre class="output" tabindex="0"><code>2488 bytes</code></pre>
 </div>
 </div>
 </div>
@@ -6379,7 +6371,7 @@ <h3 class="callout-title">Exercise 2: Parallelization</h3>
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 <p>Use the function <code>system.time</code> to obtain the runtime of
 each job.</p>
@@ -6392,9 +6384,9 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
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 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
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 </h3>
 <pre class="downlit sourceCode r">
diff --git a/instructor/cell_type_annotation.html b/instructor/cell_type_annotation.html
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@@ -518,7 +518,7 @@ <h3 class="callout-title">Challenge</h3>
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 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>We see in the help documentation for <code>?clusterCells</code> that
 all of the clustering algorithm details are handled through the
@@ -712,7 +712,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
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 <div class="accordion-body">
 <p>You can see that at least among the top markers, cluster 6 (pale
 green) tends to have the least separation from cluster 1.</p>
@@ -1007,7 +1007,7 @@ <h3 class="callout-title">Challenge</h3>
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@@ -1415,7 +1415,7 @@ <h3 class="callout-title">Exercise 1: Clustering</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
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 </button>
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 <div class="accordion-body">
 <p>The <code>NNGraphParam</code> constructor has an argument
 <code>cluster.args</code>. This allows to specify arguments passed on to
@@ -1432,7 +1432,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb46">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1470,7 +1470,7 @@ <h3 class="callout-title">Exercise 2: Reference marker genes</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
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 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb47">
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@@ -1543,7 +1543,7 @@ <h3 class="callout-title">Extension Challenge 1: Group pair comparisons</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
   <h4 class="accordion-header" id="headingSolution7"> Show me the solution </h4>
 </button>
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 <div class="accordion-body">
 <p>One important reason why is because averages over all other clusters
 can be sensitive to the cell type composition. If a rare cell type shows
@@ -1577,7 +1577,7 @@ <h3 class="callout-title">Extension Challenge 2: Parallelizing SingleR</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
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 </button>
-<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
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 <div class="accordion-body">
 <p>Use <code>BiocParallel</code> and the <code>BPPARAM</code> argument!
 This example will set it to use four cores on your laptop, but you can
@@ -1619,7 +1619,7 @@ <h3 class="callout-title">Extension Challenge 3: Critical inspection of diagnost
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
   <h4 class="accordion-header" id="headingSolution9"> Show me the solution </h4>
 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" data-bs-parent="#accordionSolution9" aria-labelledby="headingSolution9">
+<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
 <div class="accordion-body">
 <p>The example that jumps out most strongly to the eye is ExE endoderm,
 which doesn’t show clear separate modes. Simultaneously, Endothelium
diff --git a/instructor/eda_qc.html b/instructor/eda_qc.html
index 28c6a89..fb816cd 100644
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@@ -499,7 +499,7 @@ <h3 class="callout-title">Challenge</h3>
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 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
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 <div class="accordion-body">
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@@ -580,7 +580,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Setting the Random Seed </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <p>Whenever your code involves the generation of random numbers, it’s a
 good practice to set the random seed in R with
@@ -799,7 +799,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>You set <code>nmads = 4</code> like so:</p>
 <div class="codewrapper sourceCode" id="cb24">
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 </button>
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@@ -1183,7 +1183,7 @@ <h3 class="callout-title">Challenge</h3>
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 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
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 <p><code>modelGeneVar()</code> can take a <code>block</code>
 argument.</p>
@@ -1196,7 +1196,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
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 </button>
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 <div class="accordion-body">
 <p>Use the <code>block</code> argument in the call to
 <code>modelGeneVar()</code> like so:</p>
@@ -1407,7 +1407,7 @@ <h3 class="callout-title">Challenge</h3>
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 </button>
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 <div class="codewrapper sourceCode" id="cb56">
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 </button>
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb66">
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@@ -1630,7 +1630,7 @@ <h3 class="callout-title">Exercise 2: PBMC Data</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
   <h4 class="accordion-header" id="headingSolution7"> Show me the solution </h4>
 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
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 <div class="accordion-body">
 <p>The first few lines here read the data from ExperimentHub and the
 mitochondrial genes are identified by gene symbols in the row data.
@@ -1738,7 +1738,7 @@ <h3 class="callout-title">Extension challenge 1: Spike-ins</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
   <h4 class="accordion-header" id="headingSolution8"> Show me the solution </h4>
 </button>
-<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
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 <div class="accordion-body">
 <p>Spike-ins are deliberately-introduced exogeneous RNA from an exotic
 or synthetic source at a known concentration. This provides a known
@@ -1782,7 +1782,7 @@ <h3 class="callout-title">Extension challenge 3: Reduced dimensionality represen
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
   <h4 class="accordion-header" id="headingSolution9"> Show me the solution </h4>
 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" data-bs-parent="#accordionSolution9" aria-labelledby="headingSolution9">
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 <div class="accordion-body">
 <p>Mathematically, this would require the data to fall on a
 two-dimensional plane (for linear methods like PCA) or a smooth 2D
diff --git a/instructor/index.html b/instructor/index.html
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   If you already have R and RStudio installed
   </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <ul><li>Open RStudio, and click on “Help” &gt; “Check for updates”. If a new
 version is available, quit RStudio, and download the latest version for
@@ -483,7 +483,7 @@ <h4 class="accordion-header" id="headingSolution2">
   If you don’t have R and RStudio installed
   </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <ul><li>Download R from the <a href="https://cran.r-project.org/bin/windows/base/release.htm" class="external-link">CRAN
 website</a>.</li>
@@ -514,7 +514,7 @@ <h4 class="accordion-header" id="headingSolution3">
   If you already have R and RStudio installed
   </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <ul><li>Open RStudio, and click on “Help” &gt; “Check for updates”. If a new
 version is available, quit RStudio, and download the latest version for
@@ -538,7 +538,7 @@ <h4 class="accordion-header" id="headingSolution4">
   If you don’t have R and RStudio installed
   </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <ul><li>Download R from the <a href="https://cran.r-project.org/bin/macosx/" class="external-link">CRAN website</a>.</li>
 <li>Select the <code>.pkg</code> file for the latest R version</li>
@@ -571,7 +571,7 @@ <h4 class="accordion-header" id="headingSolution5">
   Install R using your package manager and RStudio
   </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <ul><li>Follow the instructions for your distribution from <a href="https://cloud.r-project.org/bin/linux" class="external-link">CRAN</a>, they provide
 information to get the most recent version of R for common
diff --git a/instructor/large_data.html b/instructor/large_data.html
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@@ -333,7 +333,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Working with large data</h1>
-        <p>Last updated on 2024-10-02 |
+        <p>Last updated on 2024-10-04 |
 
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/large_data.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -748,7 +748,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>From <code>?MulticoreParam</code> :</p>
 <blockquote>
@@ -818,21 +818,22 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="output" tabindex="0"><code>     approx
-exact   1   2   3   4   5   6   7   8   9  10  11  12  13  14
-   1   90   0   0   0   0   0   0   0   1   0   0   0   0   0
-   2    0 143   0   1   0   0   0   0   0   0   0   0   0   0
-   3    0   0  77   0   0   0   0   0   0   0   0   0   0   0
-   4    0   0   0 397   0   0   0   0   0   0   0   0   0   0
-   5    0   0   0   0 393   0   0   2   0   0   0   5   0   0
-   6    0   0   0   0   0 204   6   0   0   0   1   0   0   0
-   7    0   0   0   0   0   0 245   0   0   1   0   0   0   0
-   8    0   0   0   0   1   0   0  93   0   0   0   0   0   0
-   9    1   0   0   0   1   0   0   0 106   0   0   0   0   0
-   10   0   0   0   0   0   0   0   0   0 116   2   1   0   0
-   11   0   0   0   0   0   0   0   0   0   2 139   0   6   0
-   12   0   0   0   0   1   0   0   0   0   0   0 210   0   0
-   13   0   0   0   0   0   0   0   0   0   0   0   0 146   0
-   14   0   0   0   0   0   0   0   0   0   0   0   0   0  20</code></pre>
+exact   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15
+   1   88   0   0   0   0   0   0   2   0   0   0   1   0   0   0
+   2    0 143   0   1   0   0   0   0   0   0   0   0   0   0   0
+   3    0   0  75   0   0   0   0   0   0   0   0   2   0   0   0
+   4    0   0   0 198   0   0   0   0   0   0   0   0 143   0   0
+   5    0   0   0   0  71   0   0   0   1   0   3 322   0   0   0
+   6    0   0   0   0   0 210   0   0   0   0   0   0   0   0   0
+   7    0   0   0   0   0   0 245   0   1   0   0   0   0   0   0
+   8    0   0   0   0  95   0   0   0   0   0   0   0   0   0   0
+   9    1   0   0   0   0   0   0 106   0   0   0   1   0   0   0
+   10   0   0   0   0   0   0   0   0 112   0  10   0   0   0   0
+   11   0   0   0   0   0   0   0   0   0 153   0   0   0   0   0
+   12   0   0   0   0   8   0   0   0   0   0 195   1   0   0   0
+   13   0   0   0   0   0   0   0   0   1   0   0   0   0 146   0
+   14   0   0   0   0   0   0   0   0   0   0   0   0   0   0  20
+   15   0   0   0  56   0   0   0   0   0   0   0   0   0   0   0</code></pre>
 </div>
 <p>The similarity of the two clusterings can be quantified by
 calculating the pairwise Rand index:</p>
@@ -962,12 +963,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="callout-inner">
 <h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
-<p>The uncertainty from approximation error is sometimes psychologically
-objectionable. “Why can’t my computer just give me the right answer?”
-One way to alleviate this feeling is to quantify the approximation error
-on a small test set like the sce we have here. Using the
-<code>ExactParam()</code> class, visualize the error in PC1 coordinates
-compared to the RSVD results.</p>
+<p>The uncertainty from approximation error is sometimes aggravating.
+“Why can’t my computer just give me the right answer?” One way to
+alleviate this feeling is to quantify the approximation error on a small
+test set like the sce we have here. Using the <code>ExactParam()</code>
+class, visualize the error in PC1 coordinates compared to the RSVD
+results.</p>
 </div>
 </div>
 </div>
@@ -976,7 +977,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>This code block calculates the exact PCA coordinates. Another thing
 to note: PC vectors are only identified up to a sign flip. We can see
@@ -1379,7 +1380,7 @@ <h3 class="callout-title">Exercise 1: Out of memory representation</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>See the <code>HDF5Array</code> function for reading from HDF5 and the
 <code>writeHDF5Array</code> function for writing to HDF5 from the <em><a href="https://bioconductor.org/packages/3.19/HDF5Array" class="external-link">HDF5Array</a></em>
@@ -1393,7 +1394,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb50">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1401,61 +1402,52 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">wt_out</span> <span class="op">&lt;-</span> <span class="fu">tempfile</span><span class="op">(</span>fileext <span class="op">=</span> <span class="st">".h5"</span><span class="op">)</span></span>
 <span></span>
-<span><span class="va">wt_counts</span> <span class="op">&lt;-</span> <span class="fu">counts</span><span class="op">(</span><span class="fu">WTChimeraData</span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></code></pre>
-</div>
-<div class="codewrapper">
-<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="error" tabindex="0"><code>Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'counts': failed to load resource
-  name: EH2973
-  title: WT chimera processed counts (sample 9)
-  reason: 1 resources failed to download</code></pre>
-</div>
-<div class="codewrapper sourceCode" id="cb52">
-<h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu">writeHDF5Array</span><span class="op">(</span><span class="va">wt_counts</span>,</span>
+<span><span class="va">wt_counts</span> <span class="op">&lt;-</span> <span class="fu">counts</span><span class="op">(</span><span class="fu">WTChimeraData</span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">writeHDF5Array</span><span class="op">(</span><span class="va">wt_counts</span>,</span>
 <span>               name <span class="op">=</span> <span class="st">"wt_counts"</span>,</span>
 <span>               file <span class="op">=</span> <span class="va">wt_out</span><span class="op">)</span></span></code></pre>
 </div>
 <div class="codewrapper">
-<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="error" tabindex="0"><code>Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'is_sparse': object 'wt_counts' not found</code></pre>
-</div>
-<div class="codewrapper sourceCode" id="cb54">
-<h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">oom_wt</span> <span class="op">&lt;-</span> <span class="fu">HDF5Array</span><span class="op">(</span><span class="va">wt_out</span>, <span class="st">"wt_counts"</span><span class="op">)</span></span></code></pre>
-</div>
-<div class="codewrapper">
-<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="error" tabindex="0"><code>Error in file_path_as_absolute(path): file '/tmp/Rtmp6Q9gmL/file1e892f562866.h5' does not exist</code></pre>
+<pre class="output" tabindex="0"><code>&lt;29453 x 30703&gt; sparse HDF5Matrix object of type "double":
+                       cell_1     cell_2     cell_3 ... cell_30702 cell_30703
+ENSMUSG00000051951          0          0          0   .          0          0
+ENSMUSG00000089699          0          0          0   .          0          0
+ENSMUSG00000102343          0          0          0   .          0          0
+ENSMUSG00000025900          0          0          0   .          0          0
+ENSMUSG00000025902          0          0          0   .          0          0
+               ...          .          .          .   .          .          .
+ENSMUSG00000095041          0          1          2   .          0          0
+ENSMUSG00000063897          0          0          0   .          0          0
+ENSMUSG00000096730          0          0          0   .          0          0
+ENSMUSG00000095742          0          0          0   .          0          0
+         tomato-td          1          0          1   .          0          0</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb56">
+<div class="codewrapper sourceCode" id="cb52">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu">object.size</span><span class="op">(</span><span class="va">wt_counts</span><span class="op">)</span></span></code></pre>
+<code class="sourceCode R"><span><span class="va">oom_wt</span> <span class="op">&lt;-</span> <span class="fu">HDF5Array</span><span class="op">(</span><span class="va">wt_out</span>, <span class="st">"wt_counts"</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">object.size</span><span class="op">(</span><span class="va">wt_counts</span><span class="op">)</span></span></code></pre>
 </div>
 <div class="codewrapper">
-<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="error" tabindex="0"><code>Error in eval(expr, envir, enclos): object 'wt_counts' not found</code></pre>
+<pre class="output" tabindex="0"><code>1520366960 bytes</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb58">
+<div class="codewrapper sourceCode" id="cb54">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu">object.size</span><span class="op">(</span><span class="va">oom_wt</span><span class="op">)</span></span></code></pre>
 </div>
 <div class="codewrapper">
-<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="error" tabindex="0"><code>Error in eval(expr, envir, enclos): object 'oom_wt' not found</code></pre>
+<pre class="output" tabindex="0"><code>2488 bytes</code></pre>
 </div>
 </div>
 </div>
@@ -1481,7 +1473,7 @@ <h3 class="callout-title">Exercise 2: Parallelization</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
 <div class="accordion-body">
 <p>Use the function <code>system.time</code> to obtain the runtime of
 each job.</p>
@@ -1494,9 +1486,9 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb60">
+<div class="codewrapper sourceCode" id="cb56">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -1618,7 +1610,7 @@ <h3 class="callout-title">Key Points</h3>
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/large_data.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/large_data.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-10-02",
+  "dateModified": "2024-10-04",
   "datePublished": "2024-10-04"
 }
 
diff --git a/instructor/multi-sample.html b/instructor/multi-sample.html
index 92d94d5..41b3eca 100644
--- a/instructor/multi-sample.html
+++ b/instructor/multi-sample.html
@@ -545,7 +545,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Samples 5 and 6 were from the same “pool” of cells. Looking at the
 documentation for the dataset under <code>?WTChimeraData</code> we see
@@ -608,7 +608,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>False. Batch-level data can be retained through confounding with
 experimental factors or poor ability to distinguish experimental effects
@@ -1057,7 +1057,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>“logFC” stands for log fold-change. <code>edgeR</code> uses a log2
 convention. Rather than reporting e.g. a 5-fold increase, it’s better to
@@ -1374,7 +1374,7 @@ <h3 class="callout-title">Exercise 1: Heatmaps</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>You can simply hand <code>pheatmap()</code> a matrix as its only
 argument. <code>pheatmap()</code> has a million options you can tweak,
@@ -1388,7 +1388,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb52">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1423,7 +1423,7 @@ <h3 class="callout-title">Exercise 2: Model specification and comparison</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
 <div class="accordion-body">
 <p>After running the second pseudobulk DGE, you can join the two
 <code>DataFrame</code>s of <code>Erythroid3</code> statistics using the
@@ -1438,7 +1438,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb53">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1521,7 +1521,7 @@ <h3 class="callout-title">Extension challenge 1: Group effects</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
 <div class="accordion-body">
 <p>It’s important to have multiple samples within each experimental
 group because it helps the batch effect correction algorithm distinguish
diff --git a/large_data.html b/large_data.html
index b892e1c..2713a39 100644
--- a/large_data.html
+++ b/large_data.html
@@ -333,7 +333,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Working with large data</h1>
-        <p>Last updated on 2024-10-02 |
+        <p>Last updated on 2024-10-04 |
 
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/large_data.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -746,7 +746,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>From <code>?MulticoreParam</code> :</p>
 <blockquote>
@@ -816,21 +816,22 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="output" tabindex="0"><code>     approx
-exact   1   2   3   4   5   6   7   8   9  10  11  12  13  14
-   1   90   0   0   0   0   0   0   0   1   0   0   0   0   0
-   2    0 143   0   1   0   0   0   0   0   0   0   0   0   0
-   3    0   0  77   0   0   0   0   0   0   0   0   0   0   0
-   4    0   0   0 397   0   0   0   0   0   0   0   0   0   0
-   5    0   0   0   0 393   0   0   2   0   0   0   5   0   0
-   6    0   0   0   0   0 204   6   0   0   0   1   0   0   0
-   7    0   0   0   0   0   0 245   0   0   1   0   0   0   0
-   8    0   0   0   0   1   0   0  93   0   0   0   0   0   0
-   9    1   0   0   0   1   0   0   0 106   0   0   0   0   0
-   10   0   0   0   0   0   0   0   0   0 116   2   1   0   0
-   11   0   0   0   0   0   0   0   0   0   2 139   0   6   0
-   12   0   0   0   0   1   0   0   0   0   0   0 210   0   0
-   13   0   0   0   0   0   0   0   0   0   0   0   0 146   0
-   14   0   0   0   0   0   0   0   0   0   0   0   0   0  20</code></pre>
+exact   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15
+   1   88   0   0   0   0   0   0   2   0   0   0   1   0   0   0
+   2    0 143   0   1   0   0   0   0   0   0   0   0   0   0   0
+   3    0   0  75   0   0   0   0   0   0   0   0   2   0   0   0
+   4    0   0   0 198   0   0   0   0   0   0   0   0 143   0   0
+   5    0   0   0   0  71   0   0   0   1   0   3 322   0   0   0
+   6    0   0   0   0   0 210   0   0   0   0   0   0   0   0   0
+   7    0   0   0   0   0   0 245   0   1   0   0   0   0   0   0
+   8    0   0   0   0  95   0   0   0   0   0   0   0   0   0   0
+   9    1   0   0   0   0   0   0 106   0   0   0   1   0   0   0
+   10   0   0   0   0   0   0   0   0 112   0  10   0   0   0   0
+   11   0   0   0   0   0   0   0   0   0 153   0   0   0   0   0
+   12   0   0   0   0   8   0   0   0   0   0 195   1   0   0   0
+   13   0   0   0   0   0   0   0   0   1   0   0   0   0 146   0
+   14   0   0   0   0   0   0   0   0   0   0   0   0   0   0  20
+   15   0   0   0  56   0   0   0   0   0   0   0   0   0   0   0</code></pre>
 </div>
 <p>The similarity of the two clusterings can be quantified by
 calculating the pairwise Rand index:</p>
@@ -960,12 +961,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="callout-inner">
 <h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
-<p>The uncertainty from approximation error is sometimes psychologically
-objectionable. “Why can’t my computer just give me the right answer?”
-One way to alleviate this feeling is to quantify the approximation error
-on a small test set like the sce we have here. Using the
-<code>ExactParam()</code> class, visualize the error in PC1 coordinates
-compared to the RSVD results.</p>
+<p>The uncertainty from approximation error is sometimes aggravating.
+“Why can’t my computer just give me the right answer?” One way to
+alleviate this feeling is to quantify the approximation error on a small
+test set like the sce we have here. Using the <code>ExactParam()</code>
+class, visualize the error in PC1 coordinates compared to the RSVD
+results.</p>
 </div>
 </div>
 </div>
@@ -974,7 +975,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>This code block calculates the exact PCA coordinates. Another thing
 to note: PC vectors are only identified up to a sign flip. We can see
@@ -1377,7 +1378,7 @@ <h3 class="callout-title">Exercise 1: Out of memory representation</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>See the <code>HDF5Array</code> function for reading from HDF5 and the
 <code>writeHDF5Array</code> function for writing to HDF5 from the <em><a href="https://bioconductor.org/packages/3.19/HDF5Array" class="external-link">HDF5Array</a></em>
@@ -1391,7 +1392,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb50">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1399,61 +1400,52 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">wt_out</span> <span class="op">&lt;-</span> <span class="fu">tempfile</span><span class="op">(</span>fileext <span class="op">=</span> <span class="st">".h5"</span><span class="op">)</span></span>
 <span></span>
-<span><span class="va">wt_counts</span> <span class="op">&lt;-</span> <span class="fu">counts</span><span class="op">(</span><span class="fu">WTChimeraData</span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></code></pre>
-</div>
-<div class="codewrapper">
-<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="error" tabindex="0"><code>Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'counts': failed to load resource
-  name: EH2973
-  title: WT chimera processed counts (sample 9)
-  reason: 1 resources failed to download</code></pre>
-</div>
-<div class="codewrapper sourceCode" id="cb52">
-<h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu">writeHDF5Array</span><span class="op">(</span><span class="va">wt_counts</span>,</span>
+<span><span class="va">wt_counts</span> <span class="op">&lt;-</span> <span class="fu">counts</span><span class="op">(</span><span class="fu">WTChimeraData</span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">writeHDF5Array</span><span class="op">(</span><span class="va">wt_counts</span>,</span>
 <span>               name <span class="op">=</span> <span class="st">"wt_counts"</span>,</span>
 <span>               file <span class="op">=</span> <span class="va">wt_out</span><span class="op">)</span></span></code></pre>
 </div>
 <div class="codewrapper">
-<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="error" tabindex="0"><code>Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'is_sparse': object 'wt_counts' not found</code></pre>
-</div>
-<div class="codewrapper sourceCode" id="cb54">
-<h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">oom_wt</span> <span class="op">&lt;-</span> <span class="fu">HDF5Array</span><span class="op">(</span><span class="va">wt_out</span>, <span class="st">"wt_counts"</span><span class="op">)</span></span></code></pre>
-</div>
-<div class="codewrapper">
-<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="error" tabindex="0"><code>Error in file_path_as_absolute(path): file '/tmp/Rtmp6Q9gmL/file1e892f562866.h5' does not exist</code></pre>
+<pre class="output" tabindex="0"><code>&lt;29453 x 30703&gt; sparse HDF5Matrix object of type "double":
+                       cell_1     cell_2     cell_3 ... cell_30702 cell_30703
+ENSMUSG00000051951          0          0          0   .          0          0
+ENSMUSG00000089699          0          0          0   .          0          0
+ENSMUSG00000102343          0          0          0   .          0          0
+ENSMUSG00000025900          0          0          0   .          0          0
+ENSMUSG00000025902          0          0          0   .          0          0
+               ...          .          .          .   .          .          .
+ENSMUSG00000095041          0          1          2   .          0          0
+ENSMUSG00000063897          0          0          0   .          0          0
+ENSMUSG00000096730          0          0          0   .          0          0
+ENSMUSG00000095742          0          0          0   .          0          0
+         tomato-td          1          0          1   .          0          0</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb56">
+<div class="codewrapper sourceCode" id="cb52">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu">object.size</span><span class="op">(</span><span class="va">wt_counts</span><span class="op">)</span></span></code></pre>
+<code class="sourceCode R"><span><span class="va">oom_wt</span> <span class="op">&lt;-</span> <span class="fu">HDF5Array</span><span class="op">(</span><span class="va">wt_out</span>, <span class="st">"wt_counts"</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">object.size</span><span class="op">(</span><span class="va">wt_counts</span><span class="op">)</span></span></code></pre>
 </div>
 <div class="codewrapper">
-<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="error" tabindex="0"><code>Error in eval(expr, envir, enclos): object 'wt_counts' not found</code></pre>
+<pre class="output" tabindex="0"><code>1520366960 bytes</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb58">
+<div class="codewrapper sourceCode" id="cb54">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu">object.size</span><span class="op">(</span><span class="va">oom_wt</span><span class="op">)</span></span></code></pre>
 </div>
 <div class="codewrapper">
-<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="error" tabindex="0"><code>Error in eval(expr, envir, enclos): object 'oom_wt' not found</code></pre>
+<pre class="output" tabindex="0"><code>2488 bytes</code></pre>
 </div>
 </div>
 </div>
@@ -1479,7 +1471,7 @@ <h3 class="callout-title">Exercise 2: Parallelization</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
 <div class="accordion-body">
 <p>Use the function <code>system.time</code> to obtain the runtime of
 each job.</p>
@@ -1492,9 +1484,9 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb60">
+<div class="codewrapper sourceCode" id="cb56">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -1616,7 +1608,7 @@ <h3 class="callout-title">Key Points</h3>
   "url": "https://ccb-hms.github.io/osca-carpentries/large_data.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/large_data.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-10-02",
+  "dateModified": "2024-10-04",
   "datePublished": "2024-10-04"
 }
 
diff --git a/md5sum.txt b/md5sum.txt
index 44ccce2..138fdf2 100644
--- a/md5sum.txt
+++ b/md5sum.txt
@@ -8,7 +8,7 @@
 "episodes/eda_qc.Rmd" "d1a9a8a578fff2b0e9566ec613da388d" "site/built/eda_qc.md" "2024-10-03"
 "episodes/cell_type_annotation.Rmd" "8fab6e0cbb60d6fe6a67a0004c5ce5ab" "site/built/cell_type_annotation.md" "2024-10-02"
 "episodes/multi-sample.Rmd" "6d47bd1941b7a83000873da8d836fba0" "site/built/multi-sample.md" "2024-10-04"
-"episodes/large_data.Rmd" "f19fa53e9e63d4cb8fe0f6ab61c8fc3a" "site/built/large_data.md" "2024-10-02"
+"episodes/large_data.Rmd" "ba9660bc24664972f540bbe5fdc34d08" "site/built/large_data.md" "2024-10-04"
 "episodes/hca.Rmd" "247c19cda5e903d2eb1a5dd547d95506" "site/built/hca.md" "2024-10-03"
 "instructors/instructor-notes.md" "205339793f625a1844a768dea8e4a9c8" "site/built/instructor-notes.md" "2024-09-24"
 "learners/reference.md" "40fc1d0be2412d2d9d434a5bc84e4de8" "site/built/reference.md" "2024-09-24"
diff --git a/multi-sample.html b/multi-sample.html
index a642ecf..fe986ce 100644
--- a/multi-sample.html
+++ b/multi-sample.html
@@ -543,7 +543,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Samples 5 and 6 were from the same “pool” of cells. Looking at the
 documentation for the dataset under <code>?WTChimeraData</code> we see
@@ -606,7 +606,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>False. Batch-level data can be retained through confounding with
 experimental factors or poor ability to distinguish experimental effects
@@ -1055,7 +1055,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>“logFC” stands for log fold-change. <code>edgeR</code> uses a log2
 convention. Rather than reporting e.g. a 5-fold increase, it’s better to
@@ -1372,7 +1372,7 @@ <h3 class="callout-title">Exercise 1: Heatmaps</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>You can simply hand <code>pheatmap()</code> a matrix as its only
 argument. <code>pheatmap()</code> has a million options you can tweak,
@@ -1386,7 +1386,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb52">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1421,7 +1421,7 @@ <h3 class="callout-title">Exercise 2: Model specification and comparison</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
 <div class="accordion-body">
 <p>After running the second pseudobulk DGE, you can join the two
 <code>DataFrame</code>s of <code>Erythroid3</code> statistics using the
@@ -1436,7 +1436,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb53">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1519,7 +1519,7 @@ <h3 class="callout-title">Extension challenge 1: Group effects</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
 <div class="accordion-body">
 <p>It’s important to have multiple samples within each experimental
 group because it helps the batch effect correction algorithm distinguish
diff --git a/pkgdown.yml b/pkgdown.yml
index f806651..eb7fc54 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,4 +2,4 @@ pandoc: 3.1.11
 pkgdown: 2.1.1
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-10-04T16:55Z
+last_built: 2024-10-04T17:44Z