diff --git a/404.html b/404.html
index 3600366..181c686 100644
--- a/404.html
+++ b/404.html
@@ -274,8 +274,8 @@ <h1>Page not found</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/404.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/404.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-02-06",
-  "datePublished": "2024-02-06"
+  "dateModified": "2024-02-08",
+  "datePublished": "2024-02-08"
 }
 
   </script><script>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index 00970c2..77482b7 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -220,7 +220,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Contributor Code of Conduct</h1>
-        <p>Last updated on 2024-02-06 |
+        <p>Last updated on 2024-02-08 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/CODE_OF_CONDUCT.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -303,8 +303,8 @@ <h1>Contributor Code of Conduct</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/CODE_OF_CONDUCT.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/CODE_OF_CONDUCT.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-02-06",
-  "datePublished": "2024-02-06"
+  "dateModified": "2024-02-08",
+  "datePublished": "2024-02-08"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index 7e252d4..747bfe1 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -220,7 +220,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Licenses</h1>
-        <p>Last updated on 2024-02-06 |
+        <p>Last updated on 2024-02-08 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/LICENSE.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -354,8 +354,8 @@ <h1>Licenses</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/LICENSE.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/LICENSE.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-02-06",
-  "datePublished": "2024-02-06"
+  "dateModified": "2024-02-08",
+  "datePublished": "2024-02-08"
 }
 
   </script><script>
diff --git a/aio.html b/aio.html
index 36d3591..acbadaf 100644
--- a/aio.html
+++ b/aio.html
@@ -258,7 +258,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
         
 <section id="aio-introduction"><p>Content from <a href="introduction.html">Using RMarkdown</a></p>
 <hr>
-<p>Last updated on 2024-02-06 |
+<p>Last updated on 2024-02-08 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/introduction.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -462,12 +462,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>Loading required package: SpatialExperiment</code></pre>
 </div>
-<div class="codewrapper">
-<h3 class="code-label">WARNING<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="warning" tabindex="0"><code>Warning: replacing previous import 'S4Arrays::makeNindexFromArrayViewport' by
-'DelayedArray::makeNindexFromArrayViewport' when loading 'HDF5Array'</code></pre>
-</div>
 <section id="introduction"><h2 class="section-heading">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
 <hr class="half-width">
@@ -500,7 +494,7 @@ <h3 class="callout-title">Challenge 1: Can you do it?<a class="anchor" aria-labe
 </h3>
 <div class="callout-content">
 <p>What is the output of this command?</p>
-<div class="codewrapper sourceCode" id="cb27">
+<div class="codewrapper sourceCode" id="cb26">
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 </h3>
 <pre class="downlit sourceCode r">
@@ -514,7 +508,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <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">Output</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">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -543,7 +537,7 @@ <h3 class="callout-title">Challenge 2: how do you nest solutions within
 <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 add a line with at least three colons and a
 <code>solution</code> tag.</p>
@@ -555,7 +549,7 @@ <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </h2>
 <hr class="half-width">
 <p>You can also include figures generated from R Markdown:</p>
-<div class="codewrapper sourceCode" id="cb29">
+<div class="codewrapper sourceCode" id="cb28">
 <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">
@@ -622,7 +616,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
  -->
 </section></section><section id="aio-intro-sce"><p>Content from <a href="intro-sce.html">Introduction to Bioconductor and the SingleCellExperiment class</a></p>
 <hr>
-<p>Last updated on 2024-02-06 |
+<p>Last updated on 2024-02-08 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/intro-sce.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -686,29 +680,24 @@ <h1 id="the-singlecellexperiment-class">The <code>SingleCellExperiment</code> cl
 <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">sce</span> <span class="op">&lt;-</span> <span class="fu">WTChimeraData</span><span class="op">(</span>samples<span class="op">=</span><span class="fl">5</span><span class="op">)</span></span></code></pre>
+<code class="sourceCode R"><span><span class="va">sce</span> <span class="op">&lt;-</span> <span class="fu">WTChimeraData</span><span class="op">(</span>samples<span class="op">=</span><span class="fl">5</span><span class="op">)</span></span>
+<span><span class="va">sce</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 `collect()`:
-! Failed to collect lazy table.
-Caused by error in `db_collect()` at dbplyr/R/verb-compute.R:131:2:
-! Arguments in `...` must be used.
-✖ Problematic argument:
-• ..1 = Inf
-ℹ Did you misspell an argument name?</code></pre>
-</div>
-<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>
-</h3>
-<pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">sce</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 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>class: SingleCellExperiment 
+dim: 29453 2411 
+metadata(0):
+assays(1): counts
+rownames(29453): ENSMUSG00000051951 ENSMUSG00000089699 ...
+  ENSMUSG00000095742 tomato-td
+rowData names(2): ENSEMBL SYMBOL
+colnames(2411): cell_9769 cell_9770 ... cell_12178 cell_12179
+colData names(11): cell barcode ... doub.density sizeFactor
+reducedDimNames(2): pca.corrected.E7.5 pca.corrected.E8.5
+mainExpName: NULL
+altExpNames(0):</code></pre>
 </div>
 <p>We can think of this (and other) class as a <em>container</em>, that
 contains several different pieces of data in so-called
@@ -732,27 +721,31 @@ <h2 id="the-assays">The <code>assays</code>
 <code>assay</code> function. If one of these matrices is called
 “counts”, we can use the special <code>counts</code> getter (and the
 analogous <code>logcounts</code>).</p>
-<div class="codewrapper sourceCode" id="cb6">
+<div class="codewrapper sourceCode" id="cb4">
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 </h3>
 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu">identical</span><span class="op">(</span><span class="fu">assay</span><span class="op">(</span><span class="va">sce</span><span class="op">)</span>, <span class="fu">counts</span><span class="op">(</span><span class="va">sce</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 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 h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'assay': object 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>[1] TRUE</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb8">
+<div class="codewrapper sourceCode" id="cb6">
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 </h3>
 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu">counts</span><span class="op">(</span><span class="va">sce</span><span class="op">)</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">3</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 h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'counts': object 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>3 x 3 sparse Matrix of class "dgTMatrix"
+                   cell_9769 cell_9770 cell_9771
+ENSMUSG00000051951         .         .         .
+ENSMUSG00000089699         .         .         .
+ENSMUSG00000102343         .         .         .</code></pre>
 </div>
 <p>You will notice that in this case we have a sparse matrix of class
 “dgTMatrix” inside the object. More generally, any “matrix-like” object
@@ -767,61 +760,142 @@ <h2 id="the-coldata-and-rowdata">The <code>colData</code> and <code>rowData</cod
 the rows of your assay, respectively.</p>
 <p>One can interact with them as usual, e.g., by extracting columns or
 adding additional variables as columns.</p>
-<div class="codewrapper sourceCode" id="cb10">
+<div class="codewrapper sourceCode" id="cb8">
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 </h3>
 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu">colData</span><span class="op">(</span><span class="va">sce</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 h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colData': object 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>DataFrame with 2411 rows and 11 columns
+                  cell          barcode    sample       stage    tomato
+           &lt;character&gt;      &lt;character&gt; &lt;integer&gt; &lt;character&gt; &lt;logical&gt;
+cell_9769    cell_9769 AAACCTGAGACTGTAA         5        E8.5      TRUE
+cell_9770    cell_9770 AAACCTGAGATGCCTT         5        E8.5      TRUE
+cell_9771    cell_9771 AAACCTGAGCAGCCTC         5        E8.5      TRUE
+cell_9772    cell_9772 AAACCTGCATACTCTT         5        E8.5      TRUE
+cell_9773    cell_9773 AAACGGGTCAACACCA         5        E8.5      TRUE
+...                ...              ...       ...         ...       ...
+cell_12175  cell_12175 TTTGGTTAGTCCGTAT         5        E8.5      TRUE
+cell_12176  cell_12176 TTTGGTTAGTGTTGAA         5        E8.5      TRUE
+cell_12177  cell_12177 TTTGGTTGTTAAAGAC         5        E8.5      TRUE
+cell_12178  cell_12178 TTTGGTTTCAGTCAGT         5        E8.5      TRUE
+cell_12179  cell_12179 TTTGGTTTCGCCATAA         5        E8.5      TRUE
+                pool stage.mapped        celltype.mapped closest.cell
+           &lt;integer&gt;  &lt;character&gt;            &lt;character&gt;  &lt;character&gt;
+cell_9769          3        E8.25             Mesenchyme   cell_24159
+cell_9770          3         E8.5            Endothelium   cell_96660
+cell_9771          3         E8.5              Allantois  cell_134982
+cell_9772          3         E8.5             Erythroid3  cell_133892
+cell_9773          3        E8.25             Erythroid1   cell_76296
+...              ...          ...                    ...          ...
+cell_12175         3         E8.5             Erythroid3  cell_138060
+cell_12176         3         E8.5 Forebrain/Midbrain/H..   cell_72709
+cell_12177         3        E8.25       Surface ectoderm  cell_100275
+cell_12178         3        E8.25             Erythroid2   cell_70906
+cell_12179         3         E8.5            Spinal cord  cell_102334
+           doub.density sizeFactor
+              &lt;numeric&gt;  &lt;numeric&gt;
+cell_9769    0.02985045    1.41243
+cell_9770    0.00172753    1.22757
+cell_9771    0.01338013    1.15439
+cell_9772    0.00218402    1.28676
+cell_9773    0.00211723    1.78719
+...                 ...        ...
+cell_12175   0.00129403   1.219506
+cell_12176   0.01833074   1.095753
+cell_12177   0.03104037   0.910728
+cell_12178   0.00169483   2.061701
+cell_12179   0.03767894   1.798687</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb12">
+<div class="codewrapper sourceCode" id="cb10">
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 </h3>
 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu">rowData</span><span class="op">(</span><span class="va">sce</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 h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'rowData': object 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>DataFrame with 29453 rows and 2 columns
+                              ENSEMBL         SYMBOL
+                          &lt;character&gt;    &lt;character&gt;
+ENSMUSG00000051951 ENSMUSG00000051951           Xkr4
+ENSMUSG00000089699 ENSMUSG00000089699         Gm1992
+ENSMUSG00000102343 ENSMUSG00000102343        Gm37381
+ENSMUSG00000025900 ENSMUSG00000025900            Rp1
+ENSMUSG00000025902 ENSMUSG00000025902          Sox17
+...                               ...            ...
+ENSMUSG00000095041 ENSMUSG00000095041     AC149090.1
+ENSMUSG00000063897 ENSMUSG00000063897          DHRSX
+ENSMUSG00000096730 ENSMUSG00000096730       Vmn2r122
+ENSMUSG00000095742 ENSMUSG00000095742 CAAA01147332.1
+tomato-td                   tomato-td      tomato-td</code></pre>
 </div>
 <p>Note the <code>$</code> short cut.</p>
-<div class="codewrapper sourceCode" id="cb14">
+<div class="codewrapper sourceCode" id="cb12">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu">identical</span><span class="op">(</span><span class="fu">colData</span><span class="op">(</span><span class="va">sce</span><span class="op">)</span><span class="op">$</span><span class="va">sum</span>, <span class="va">sce</span><span class="op">$</span><span class="va">sum</span><span class="op">)</span></span></code></pre>
 </div>
 <div class="codewrapper">
-<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="error" tabindex="0"><code>Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colData': object 'sce' not found</code></pre>
-</div>
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-<h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">sce</span><span class="op">$</span><span class="va">my_sum</span> <span class="op">&lt;-</span> <span class="fu">colSums</span><span class="op">(</span><span class="fu">counts</span><span class="op">(</span><span class="va">sce</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 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 h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colSums': error in evaluating the argument 'object' in selecting a method for function 'counts': object 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>[1] TRUE</code></pre>
 </div>
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+<div class="codewrapper sourceCode" id="cb14">
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 </h3>
 <pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu">colData</span><span class="op">(</span><span class="va">sce</span><span class="op">)</span></span></code></pre>
+<code class="sourceCode R"><span><span class="va">sce</span><span class="op">$</span><span class="va">my_sum</span> <span class="op">&lt;-</span> <span class="fu">colSums</span><span class="op">(</span><span class="fu">counts</span><span class="op">(</span><span class="va">sce</span><span class="op">)</span><span class="op">)</span></span>
+<span><span class="fu">colData</span><span class="op">(</span><span class="va">sce</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 h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colData': object 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>DataFrame with 2411 rows and 12 columns
+                  cell          barcode    sample       stage    tomato
+           &lt;character&gt;      &lt;character&gt; &lt;integer&gt; &lt;character&gt; &lt;logical&gt;
+cell_9769    cell_9769 AAACCTGAGACTGTAA         5        E8.5      TRUE
+cell_9770    cell_9770 AAACCTGAGATGCCTT         5        E8.5      TRUE
+cell_9771    cell_9771 AAACCTGAGCAGCCTC         5        E8.5      TRUE
+cell_9772    cell_9772 AAACCTGCATACTCTT         5        E8.5      TRUE
+cell_9773    cell_9773 AAACGGGTCAACACCA         5        E8.5      TRUE
+...                ...              ...       ...         ...       ...
+cell_12175  cell_12175 TTTGGTTAGTCCGTAT         5        E8.5      TRUE
+cell_12176  cell_12176 TTTGGTTAGTGTTGAA         5        E8.5      TRUE
+cell_12177  cell_12177 TTTGGTTGTTAAAGAC         5        E8.5      TRUE
+cell_12178  cell_12178 TTTGGTTTCAGTCAGT         5        E8.5      TRUE
+cell_12179  cell_12179 TTTGGTTTCGCCATAA         5        E8.5      TRUE
+                pool stage.mapped        celltype.mapped closest.cell
+           &lt;integer&gt;  &lt;character&gt;            &lt;character&gt;  &lt;character&gt;
+cell_9769          3        E8.25             Mesenchyme   cell_24159
+cell_9770          3         E8.5            Endothelium   cell_96660
+cell_9771          3         E8.5              Allantois  cell_134982
+cell_9772          3         E8.5             Erythroid3  cell_133892
+cell_9773          3        E8.25             Erythroid1   cell_76296
+...              ...          ...                    ...          ...
+cell_12175         3         E8.5             Erythroid3  cell_138060
+cell_12176         3         E8.5 Forebrain/Midbrain/H..   cell_72709
+cell_12177         3        E8.25       Surface ectoderm  cell_100275
+cell_12178         3        E8.25             Erythroid2   cell_70906
+cell_12179         3         E8.5            Spinal cord  cell_102334
+           doub.density sizeFactor    my_sum
+              &lt;numeric&gt;  &lt;numeric&gt; &lt;numeric&gt;
+cell_9769    0.02985045    1.41243     27577
+cell_9770    0.00172753    1.22757     29309
+cell_9771    0.01338013    1.15439     28795
+cell_9772    0.00218402    1.28676     34794
+cell_9773    0.00211723    1.78719     38300
+...                 ...        ...       ...
+cell_12175   0.00129403   1.219506     26680
+cell_12176   0.01833074   1.095753     19013
+cell_12177   0.03104037   0.910728     24627
+cell_12178   0.00169483   2.061701     46162
+cell_12179   0.03767894   1.798687     38398</code></pre>
 </div>
 </div>
 <div class="section level2">
@@ -835,16 +909,17 @@ <h2 id="the-reduceddims">The <code>reducedDims</code>
 <p>One of the peculiarity of SingleCellExperiment is its ability to
 store reduced dimension matrices within the object. These may include
 PCA, t-SNE, UMAP, etc.</p>
-<div class="codewrapper sourceCode" id="cb20">
+<div class="codewrapper sourceCode" id="cb16">
 <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">reducedDims</span><span class="op">(</span><span class="va">sce</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 h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'reducedDims': object 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>List of length 2
+names(2): pca.corrected.E7.5 pca.corrected.E8.5</code></pre>
 </div>
 <p>As for the other slots, we have the usual setter/getter, but it is
 somewhat rare to interact directly with these functions.</p>
@@ -856,7 +931,7 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 <em>indirectly</em> from the objects. Note that one could obtain the
 same results (somewhat less efficiently) by extracting the corresponding
 <code>reducedDim</code> matrix and <code>ggplot</code>.</p>
-<div class="codewrapper sourceCode" id="cb22">
+<div class="codewrapper sourceCode" id="cb18">
 <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">
@@ -872,18 +947,18 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>Loading required package: ggplot2</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb25">
+<div class="codewrapper sourceCode" id="cb21">
 <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">plotReducedDim</span><span class="op">(</span><span class="va">sce</span>, <span class="st">"pca.corrected.E8.5"</span>, colour_by <span class="op">=</span> <span class="st">"celltype.mapped"</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">WARNING<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 'reducedDim': object 'sce' not found</code></pre>
+<pre class="warning" tabindex="0"><code>Warning: Removed 131 rows containing missing values (`geom_point()`).</code></pre>
 </div>
-<div id="exercise-1" class="callout challenge">
+<figure><img src="fig/intro-sce-rendered-unnamed-chunk-7-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><div id="exercise-1" class="callout challenge">
 <div class="callout-square">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
@@ -903,7 +978,7 @@ <h3 class="callout-title">Exercise 1<a class="anchor" aria-label="anchor" href="
 <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>SingleCellExperiment</code> function can be used to create
 a new SingleCellExperiment object</p>
@@ -916,7 +991,7 @@ <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="#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>TODO</p>
 </div>
@@ -944,7 +1019,7 @@ <h3 class="callout-title">Exercise 2<a class="anchor" aria-label="anchor" href="
 <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>TODO</p>
 </div>
@@ -1026,8 +1101,8 @@ <h1 id="further-reading">Further Reading<a class="anchor" aria-label="anchor" hr
   "url": "https://ccb-hms.github.io/osca-carpentries/aio.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/aio.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-02-06",
-  "datePublished": "2024-02-06"
+  "dateModified": "2024-02-08",
+  "datePublished": "2024-02-08"
 }
 
   </script><script>
diff --git a/fig/intro-sce-rendered-unnamed-chunk-7-1.png b/fig/intro-sce-rendered-unnamed-chunk-7-1.png
new file mode 100644
index 0000000..2788905
Binary files /dev/null and b/fig/intro-sce-rendered-unnamed-chunk-7-1.png differ
diff --git a/images.html b/images.html
index 977dd93..85259b8 100644
--- a/images.html
+++ b/images.html
@@ -268,7 +268,9 @@ <h3 id="introduction-figure-2">Figure 2</h3>
 <figure><img src="https://raw.githubusercontent.com/carpentries/logo/master/Badge_Carpentries.svg" alt="Blue Carpentries hex person logo with no text." class="figure mx-auto d-block"><figcaption>You belong in The Carpentries!</figcaption></figure><hr></section><section id="intro-sce"><h2 class="section-heading"><a href="intro-sce.html">Introduction to Bioconductor and the SingleCellExperiment classSetup<a class="anchor" aria-label="anchor" href="#setup"></a>The <code>SingleCellExperiment</code> class<a class="anchor" aria-label="anchor" href="#the-singlecellexperiment-class"></a>Further Reading<a class="anchor" aria-label="anchor" href="#further-reading"></a></a></h2>
 <hr class="half-width">
 <h3 id="intro-sce-figure-1">Figure 1</h3>
-<figure><img src="http://bioconductor.org/books/3.17/OSCA.intro/images/SingleCellExperiment.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><hr></section>
+<figure><img src="http://bioconductor.org/books/3.17/OSCA.intro/images/SingleCellExperiment.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><hr>
+<h3 id="intro-sce-figure-2">Figure 2</h3>
+<figure><img src="fig/intro-sce-rendered-unnamed-chunk-7-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><hr></section>
 </div>
     </main>
 </div>
@@ -316,8 +318,8 @@ <h3 id="intro-sce-figure-1">Figure 1</h3>
   "url": "https://ccb-hms.github.io/osca-carpentries/images.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/images.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-02-06",
-  "datePublished": "2024-02-06"
+  "dateModified": "2024-02-08",
+  "datePublished": "2024-02-08"
 }
 
   </script><script>
diff --git a/index.html b/index.html
index 0e337a6..443a4df 100644
--- a/index.html
+++ b/index.html
@@ -350,8 +350,8 @@ <h4 class="accordion-header" id="headingSolution3">Linux</h4>
   "url": "https://ccb-hms.github.io/osca-carpentries/index.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/index.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-02-06",
-  "datePublished": "2024-02-06"
+  "dateModified": "2024-02-08",
+  "datePublished": "2024-02-08"
 }
 
   </script><script>
diff --git a/instructor-notes.html b/instructor-notes.html
index 40840ca..59ced1f 100644
--- a/instructor-notes.html
+++ b/instructor-notes.html
@@ -312,8 +312,8 @@ <h1>Instructor Notes</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor-notes.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor-notes.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-02-06",
-  "datePublished": "2024-02-06"
+  "dateModified": "2024-02-08",
+  "datePublished": "2024-02-08"
 }
 
   </script><script>
diff --git a/instructor/404.html b/instructor/404.html
index 50d0096..5a96391 100644
--- a/instructor/404.html
+++ b/instructor/404.html
@@ -274,8 +274,8 @@ <h1>Page not found</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/404.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/404.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-02-06",
-  "datePublished": "2024-02-06"
+  "dateModified": "2024-02-08",
+  "datePublished": "2024-02-08"
 }
 
   </script><script>
diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index 51a7dd4..d3a0cac 100644
--- a/instructor/CODE_OF_CONDUCT.html
+++ b/instructor/CODE_OF_CONDUCT.html
@@ -220,7 +220,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Contributor Code of Conduct</h1>
-        <p>Last updated on 2024-02-06 |
+        <p>Last updated on 2024-02-08 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/CODE_OF_CONDUCT.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -305,8 +305,8 @@ <h1>Contributor Code of Conduct</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/CODE_OF_CONDUCT.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/CODE_OF_CONDUCT.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-02-06",
-  "datePublished": "2024-02-06"
+  "dateModified": "2024-02-08",
+  "datePublished": "2024-02-08"
 }
 
   </script><script>
diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index 30f6a0a..106ea66 100644
--- a/instructor/LICENSE.html
+++ b/instructor/LICENSE.html
@@ -220,7 +220,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Licenses</h1>
-        <p>Last updated on 2024-02-06 |
+        <p>Last updated on 2024-02-08 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/LICENSE.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -356,8 +356,8 @@ <h1>Licenses</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/LICENSE.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/LICENSE.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-02-06",
-  "datePublished": "2024-02-06"
+  "dateModified": "2024-02-08",
+  "datePublished": "2024-02-08"
 }
 
   </script><script>
diff --git a/instructor/aio.html b/instructor/aio.html
index 4eb00f8..adc6943 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -260,7 +260,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
         
 <section id="aio-introduction"><p>Content from <a href="introduction.html">Using RMarkdown</a></p>
 <hr>
-<p>Last updated on 2024-02-06 |
+<p>Last updated on 2024-02-08 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/introduction.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>
@@ -465,12 +465,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>Loading required package: SpatialExperiment</code></pre>
 </div>
-<div class="codewrapper">
-<h3 class="code-label">WARNING<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="warning" tabindex="0"><code>Warning: replacing previous import 'S4Arrays::makeNindexFromArrayViewport' by
-'DelayedArray::makeNindexFromArrayViewport' when loading 'HDF5Array'</code></pre>
-</div>
 <section id="introduction"><h2 class="section-heading">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
 <hr class="half-width">
@@ -500,7 +494,7 @@ <h3 class="code-label">WARNING<i aria-hidden="true" data-feather="chevron-left">
   <h3 class="accordion-header" id="headingInstructor1">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="edit-2"></i></div>Instructor Note</h3>
 </button>
-<div id="collapseInstructor1" class="accordion-collapse collapse" data-bs-parent="#accordionInstructor1" aria-labelledby="headingInstructor1">
+<div id="collapseInstructor1" class="accordion-collapse collapse" aria-labelledby="headingInstructor1" data-bs-parent="#accordionInstructor1">
 <div class="accordion-body">
 <p>Inline instructor notes can help inform instructors of timing
 challenges associated with the lessons. They appear in the “Instructor
@@ -518,7 +512,7 @@ <h3 class="callout-title">Challenge 1: Can you do it?<a class="anchor" aria-labe
 </h3>
 <div class="callout-content">
 <p>What is the output of this command?</p>
-<div class="codewrapper sourceCode" id="cb27">
+<div class="codewrapper sourceCode" id="cb26">
 <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">
@@ -532,7 +526,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <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">Output</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">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -561,7 +555,7 @@ <h3 class="callout-title">Challenge 2: how do you nest solutions within
 <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 add a line with at least three colons and a
 <code>solution</code> tag.</p>
@@ -573,7 +567,7 @@ <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </h2>
 <hr class="half-width">
 <p>You can also include figures generated from R Markdown:</p>
-<div class="codewrapper sourceCode" id="cb29">
+<div class="codewrapper sourceCode" id="cb28">
 <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">
@@ -640,7 +634,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
  -->
 </section></section><section id="aio-intro-sce"><p>Content from <a href="intro-sce.html">Introduction to Bioconductor and the SingleCellExperiment class</a></p>
 <hr>
-<p>Last updated on 2024-02-06 |
+<p>Last updated on 2024-02-08 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/intro-sce.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>
@@ -705,29 +699,24 @@ <h1 id="the-singlecellexperiment-class">The <code>SingleCellExperiment</code> cl
 <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">sce</span> <span class="op">&lt;-</span> <span class="fu">WTChimeraData</span><span class="op">(</span>samples<span class="op">=</span><span class="fl">5</span><span class="op">)</span></span></code></pre>
+<code class="sourceCode R"><span><span class="va">sce</span> <span class="op">&lt;-</span> <span class="fu">WTChimeraData</span><span class="op">(</span>samples<span class="op">=</span><span class="fl">5</span><span class="op">)</span></span>
+<span><span class="va">sce</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 `collect()`:
-! Failed to collect lazy table.
-Caused by error in `db_collect()` at dbplyr/R/verb-compute.R:131:2:
-! Arguments in `...` must be used.
-✖ Problematic argument:
-• ..1 = Inf
-ℹ Did you misspell an argument name?</code></pre>
-</div>
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-<pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">sce</span></span></code></pre>
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-<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 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>class: SingleCellExperiment 
+dim: 29453 2411 
+metadata(0):
+assays(1): counts
+rownames(29453): ENSMUSG00000051951 ENSMUSG00000089699 ...
+  ENSMUSG00000095742 tomato-td
+rowData names(2): ENSEMBL SYMBOL
+colnames(2411): cell_9769 cell_9770 ... cell_12178 cell_12179
+colData names(11): cell barcode ... doub.density sizeFactor
+reducedDimNames(2): pca.corrected.E7.5 pca.corrected.E8.5
+mainExpName: NULL
+altExpNames(0):</code></pre>
 </div>
 <p>We can think of this (and other) class as a <em>container</em>, that
 contains several different pieces of data in so-called
@@ -751,27 +740,31 @@ <h2 id="the-assays">The <code>assays</code>
 <code>assay</code> function. If one of these matrices is called
 “counts”, we can use the special <code>counts</code> getter (and the
 analogous <code>logcounts</code>).</p>
-<div class="codewrapper sourceCode" id="cb6">
+<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>
 </h3>
 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu">identical</span><span class="op">(</span><span class="fu">assay</span><span class="op">(</span><span class="va">sce</span><span class="op">)</span>, <span class="fu">counts</span><span class="op">(</span><span class="va">sce</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 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 h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'assay': object 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>[1] TRUE</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb8">
+<div class="codewrapper sourceCode" id="cb6">
 <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">counts</span><span class="op">(</span><span class="va">sce</span><span class="op">)</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">3</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 h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'counts': object 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>3 x 3 sparse Matrix of class "dgTMatrix"
+                   cell_9769 cell_9770 cell_9771
+ENSMUSG00000051951         .         .         .
+ENSMUSG00000089699         .         .         .
+ENSMUSG00000102343         .         .         .</code></pre>
 </div>
 <p>You will notice that in this case we have a sparse matrix of class
 “dgTMatrix” inside the object. More generally, any “matrix-like” object
@@ -786,61 +779,142 @@ <h2 id="the-coldata-and-rowdata">The <code>colData</code> and <code>rowData</cod
 the rows of your assay, respectively.</p>
 <p>One can interact with them as usual, e.g., by extracting columns or
 adding additional variables as columns.</p>
-<div class="codewrapper sourceCode" id="cb10">
+<div class="codewrapper sourceCode" id="cb8">
 <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">colData</span><span class="op">(</span><span class="va">sce</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 h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colData': object 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>DataFrame with 2411 rows and 11 columns
+                  cell          barcode    sample       stage    tomato
+           &lt;character&gt;      &lt;character&gt; &lt;integer&gt; &lt;character&gt; &lt;logical&gt;
+cell_9769    cell_9769 AAACCTGAGACTGTAA         5        E8.5      TRUE
+cell_9770    cell_9770 AAACCTGAGATGCCTT         5        E8.5      TRUE
+cell_9771    cell_9771 AAACCTGAGCAGCCTC         5        E8.5      TRUE
+cell_9772    cell_9772 AAACCTGCATACTCTT         5        E8.5      TRUE
+cell_9773    cell_9773 AAACGGGTCAACACCA         5        E8.5      TRUE
+...                ...              ...       ...         ...       ...
+cell_12175  cell_12175 TTTGGTTAGTCCGTAT         5        E8.5      TRUE
+cell_12176  cell_12176 TTTGGTTAGTGTTGAA         5        E8.5      TRUE
+cell_12177  cell_12177 TTTGGTTGTTAAAGAC         5        E8.5      TRUE
+cell_12178  cell_12178 TTTGGTTTCAGTCAGT         5        E8.5      TRUE
+cell_12179  cell_12179 TTTGGTTTCGCCATAA         5        E8.5      TRUE
+                pool stage.mapped        celltype.mapped closest.cell
+           &lt;integer&gt;  &lt;character&gt;            &lt;character&gt;  &lt;character&gt;
+cell_9769          3        E8.25             Mesenchyme   cell_24159
+cell_9770          3         E8.5            Endothelium   cell_96660
+cell_9771          3         E8.5              Allantois  cell_134982
+cell_9772          3         E8.5             Erythroid3  cell_133892
+cell_9773          3        E8.25             Erythroid1   cell_76296
+...              ...          ...                    ...          ...
+cell_12175         3         E8.5             Erythroid3  cell_138060
+cell_12176         3         E8.5 Forebrain/Midbrain/H..   cell_72709
+cell_12177         3        E8.25       Surface ectoderm  cell_100275
+cell_12178         3        E8.25             Erythroid2   cell_70906
+cell_12179         3         E8.5            Spinal cord  cell_102334
+           doub.density sizeFactor
+              &lt;numeric&gt;  &lt;numeric&gt;
+cell_9769    0.02985045    1.41243
+cell_9770    0.00172753    1.22757
+cell_9771    0.01338013    1.15439
+cell_9772    0.00218402    1.28676
+cell_9773    0.00211723    1.78719
+...                 ...        ...
+cell_12175   0.00129403   1.219506
+cell_12176   0.01833074   1.095753
+cell_12177   0.03104037   0.910728
+cell_12178   0.00169483   2.061701
+cell_12179   0.03767894   1.798687</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb12">
+<div class="codewrapper sourceCode" id="cb10">
 <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">rowData</span><span class="op">(</span><span class="va">sce</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 h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'rowData': object 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>DataFrame with 29453 rows and 2 columns
+                              ENSEMBL         SYMBOL
+                          &lt;character&gt;    &lt;character&gt;
+ENSMUSG00000051951 ENSMUSG00000051951           Xkr4
+ENSMUSG00000089699 ENSMUSG00000089699         Gm1992
+ENSMUSG00000102343 ENSMUSG00000102343        Gm37381
+ENSMUSG00000025900 ENSMUSG00000025900            Rp1
+ENSMUSG00000025902 ENSMUSG00000025902          Sox17
+...                               ...            ...
+ENSMUSG00000095041 ENSMUSG00000095041     AC149090.1
+ENSMUSG00000063897 ENSMUSG00000063897          DHRSX
+ENSMUSG00000096730 ENSMUSG00000096730       Vmn2r122
+ENSMUSG00000095742 ENSMUSG00000095742 CAAA01147332.1
+tomato-td                   tomato-td      tomato-td</code></pre>
 </div>
 <p>Note the <code>$</code> short cut.</p>
-<div class="codewrapper sourceCode" id="cb14">
+<div class="codewrapper sourceCode" id="cb12">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu">identical</span><span class="op">(</span><span class="fu">colData</span><span class="op">(</span><span class="va">sce</span><span class="op">)</span><span class="op">$</span><span class="va">sum</span>, <span class="va">sce</span><span class="op">$</span><span class="va">sum</span><span class="op">)</span></span></code></pre>
 </div>
 <div class="codewrapper">
-<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="error" tabindex="0"><code>Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colData': object 'sce' not found</code></pre>
-</div>
-<div class="codewrapper sourceCode" id="cb16">
-<h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">sce</span><span class="op">$</span><span class="va">my_sum</span> <span class="op">&lt;-</span> <span class="fu">colSums</span><span class="op">(</span><span class="fu">counts</span><span class="op">(</span><span class="va">sce</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 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 h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colSums': error in evaluating the argument 'object' in selecting a method for function 'counts': object 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>[1] TRUE</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb18">
+<div class="codewrapper sourceCode" id="cb14">
 <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">colData</span><span class="op">(</span><span class="va">sce</span><span class="op">)</span></span></code></pre>
+<code class="sourceCode R"><span><span class="va">sce</span><span class="op">$</span><span class="va">my_sum</span> <span class="op">&lt;-</span> <span class="fu">colSums</span><span class="op">(</span><span class="fu">counts</span><span class="op">(</span><span class="va">sce</span><span class="op">)</span><span class="op">)</span></span>
+<span><span class="fu">colData</span><span class="op">(</span><span class="va">sce</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 h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colData': object 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>DataFrame with 2411 rows and 12 columns
+                  cell          barcode    sample       stage    tomato
+           &lt;character&gt;      &lt;character&gt; &lt;integer&gt; &lt;character&gt; &lt;logical&gt;
+cell_9769    cell_9769 AAACCTGAGACTGTAA         5        E8.5      TRUE
+cell_9770    cell_9770 AAACCTGAGATGCCTT         5        E8.5      TRUE
+cell_9771    cell_9771 AAACCTGAGCAGCCTC         5        E8.5      TRUE
+cell_9772    cell_9772 AAACCTGCATACTCTT         5        E8.5      TRUE
+cell_9773    cell_9773 AAACGGGTCAACACCA         5        E8.5      TRUE
+...                ...              ...       ...         ...       ...
+cell_12175  cell_12175 TTTGGTTAGTCCGTAT         5        E8.5      TRUE
+cell_12176  cell_12176 TTTGGTTAGTGTTGAA         5        E8.5      TRUE
+cell_12177  cell_12177 TTTGGTTGTTAAAGAC         5        E8.5      TRUE
+cell_12178  cell_12178 TTTGGTTTCAGTCAGT         5        E8.5      TRUE
+cell_12179  cell_12179 TTTGGTTTCGCCATAA         5        E8.5      TRUE
+                pool stage.mapped        celltype.mapped closest.cell
+           &lt;integer&gt;  &lt;character&gt;            &lt;character&gt;  &lt;character&gt;
+cell_9769          3        E8.25             Mesenchyme   cell_24159
+cell_9770          3         E8.5            Endothelium   cell_96660
+cell_9771          3         E8.5              Allantois  cell_134982
+cell_9772          3         E8.5             Erythroid3  cell_133892
+cell_9773          3        E8.25             Erythroid1   cell_76296
+...              ...          ...                    ...          ...
+cell_12175         3         E8.5             Erythroid3  cell_138060
+cell_12176         3         E8.5 Forebrain/Midbrain/H..   cell_72709
+cell_12177         3        E8.25       Surface ectoderm  cell_100275
+cell_12178         3        E8.25             Erythroid2   cell_70906
+cell_12179         3         E8.5            Spinal cord  cell_102334
+           doub.density sizeFactor    my_sum
+              &lt;numeric&gt;  &lt;numeric&gt; &lt;numeric&gt;
+cell_9769    0.02985045    1.41243     27577
+cell_9770    0.00172753    1.22757     29309
+cell_9771    0.01338013    1.15439     28795
+cell_9772    0.00218402    1.28676     34794
+cell_9773    0.00211723    1.78719     38300
+...                 ...        ...       ...
+cell_12175   0.00129403   1.219506     26680
+cell_12176   0.01833074   1.095753     19013
+cell_12177   0.03104037   0.910728     24627
+cell_12178   0.00169483   2.061701     46162
+cell_12179   0.03767894   1.798687     38398</code></pre>
 </div>
 </div>
 <div class="section level2">
@@ -854,16 +928,17 @@ <h2 id="the-reduceddims">The <code>reducedDims</code>
 <p>One of the peculiarity of SingleCellExperiment is its ability to
 store reduced dimension matrices within the object. These may include
 PCA, t-SNE, UMAP, etc.</p>
-<div class="codewrapper sourceCode" id="cb20">
+<div class="codewrapper sourceCode" id="cb16">
 <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">reducedDims</span><span class="op">(</span><span class="va">sce</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 h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'reducedDims': object 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>List of length 2
+names(2): pca.corrected.E7.5 pca.corrected.E8.5</code></pre>
 </div>
 <p>As for the other slots, we have the usual setter/getter, but it is
 somewhat rare to interact directly with these functions.</p>
@@ -875,7 +950,7 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 <em>indirectly</em> from the objects. Note that one could obtain the
 same results (somewhat less efficiently) by extracting the corresponding
 <code>reducedDim</code> matrix and <code>ggplot</code>.</p>
-<div class="codewrapper sourceCode" id="cb22">
+<div class="codewrapper sourceCode" id="cb18">
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 </h3>
 <pre class="downlit sourceCode r">
@@ -891,18 +966,18 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>Loading required package: ggplot2</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb25">
+<div class="codewrapper sourceCode" id="cb21">
 <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">plotReducedDim</span><span class="op">(</span><span class="va">sce</span>, <span class="st">"pca.corrected.E8.5"</span>, colour_by <span class="op">=</span> <span class="st">"celltype.mapped"</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">WARNING<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 'reducedDim': object 'sce' not found</code></pre>
+<pre class="warning" tabindex="0"><code>Warning: Removed 131 rows containing missing values (`geom_point()`).</code></pre>
 </div>
-<div id="exercise-1" class="callout challenge">
+<figure><img src="../fig/intro-sce-rendered-unnamed-chunk-7-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><div id="exercise-1" class="callout challenge">
 <div class="callout-square">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
@@ -922,7 +997,7 @@ <h3 class="callout-title">Exercise 1<a class="anchor" aria-label="anchor" href="
 <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>SingleCellExperiment</code> function can be used to create
 a new SingleCellExperiment object</p>
@@ -935,7 +1010,7 @@ <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="#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>TODO</p>
 </div>
@@ -963,7 +1038,7 @@ <h3 class="callout-title">Exercise 2<a class="anchor" aria-label="anchor" href="
 <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>TODO</p>
 </div>
@@ -1045,8 +1120,8 @@ <h1 id="further-reading">Further Reading<a class="anchor" aria-label="anchor" hr
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/aio.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/aio.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-02-06",
-  "datePublished": "2024-02-06"
+  "dateModified": "2024-02-08",
+  "datePublished": "2024-02-08"
 }
 
   </script><script>
diff --git a/instructor/images.html b/instructor/images.html
index c594c76..cd2715c 100644
--- a/instructor/images.html
+++ b/instructor/images.html
@@ -270,7 +270,9 @@ <h3 id="introduction-figure-2">Figure 2</h3>
 <figure><img src="https://raw.githubusercontent.com/carpentries/logo/master/Badge_Carpentries.svg" alt="Blue Carpentries hex person logo with no text." class="figure mx-auto d-block"><figcaption>You belong in The Carpentries!</figcaption></figure><hr></section><section id="intro-sce"><h2 class="section-heading"><a href="intro-sce.html">Introduction to Bioconductor and the SingleCellExperiment classSetup<a class="anchor" aria-label="anchor" href="#setup"></a>The <code>SingleCellExperiment</code> class<a class="anchor" aria-label="anchor" href="#the-singlecellexperiment-class"></a>Further Reading<a class="anchor" aria-label="anchor" href="#further-reading"></a></a></h2>
 <hr class="half-width">
 <h3 id="intro-sce-figure-1">Figure 1</h3>
-<figure><img src="http://bioconductor.org/books/3.17/OSCA.intro/images/SingleCellExperiment.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><hr></section>
+<figure><img src="http://bioconductor.org/books/3.17/OSCA.intro/images/SingleCellExperiment.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><hr>
+<h3 id="intro-sce-figure-2">Figure 2</h3>
+<figure><img src="../fig/intro-sce-rendered-unnamed-chunk-7-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><hr></section>
 </div>
     </main>
 </div>
@@ -318,8 +320,8 @@ <h3 id="intro-sce-figure-1">Figure 1</h3>
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/images.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/images.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-02-06",
-  "datePublished": "2024-02-06"
+  "dateModified": "2024-02-08",
+  "datePublished": "2024-02-08"
 }
 
   </script><script>
diff --git a/instructor/index.html b/instructor/index.html
index d26e330..92bd84d 100644
--- a/instructor/index.html
+++ b/instructor/index.html
@@ -377,8 +377,8 @@ <h4 class="accordion-header" id="headingSolution3">Linux</h4>
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/index.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/index.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-02-06",
-  "datePublished": "2024-02-06"
+  "dateModified": "2024-02-08",
+  "datePublished": "2024-02-08"
 }
 
   </script><script>
diff --git a/instructor/instructor-notes.html b/instructor/instructor-notes.html
index 6c2545a..7745996 100644
--- a/instructor/instructor-notes.html
+++ b/instructor/instructor-notes.html
@@ -324,8 +324,8 @@ <h3 id="introduction-headingInstructor1">
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/instructor-notes.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/instructor-notes.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-02-06",
-  "datePublished": "2024-02-06"
+  "dateModified": "2024-02-08",
+  "datePublished": "2024-02-08"
 }
 
   </script><script>
diff --git a/instructor/intro-sce.html b/instructor/intro-sce.html
index 73af9d6..c771a7c 100644
--- a/instructor/intro-sce.html
+++ b/instructor/intro-sce.html
@@ -224,7 +224,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Introduction to Bioconductor and the SingleCellExperiment class</h1>
-        <p>Last updated on 2024-02-06 |
+        <p>Last updated on 2024-02-08 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/intro-sce.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -290,29 +290,24 @@ <h1 id="the-singlecellexperiment-class">The <code>SingleCellExperiment</code> cl
 <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">sce</span> <span class="op">&lt;-</span> <span class="fu">WTChimeraData</span><span class="op">(</span>samples<span class="op">=</span><span class="fl">5</span><span class="op">)</span></span></code></pre>
+<code class="sourceCode R"><span><span class="va">sce</span> <span class="op">&lt;-</span> <span class="fu">WTChimeraData</span><span class="op">(</span>samples<span class="op">=</span><span class="fl">5</span><span class="op">)</span></span>
+<span><span class="va">sce</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 `collect()`:
-! Failed to collect lazy table.
-Caused by error in `db_collect()` at dbplyr/R/verb-compute.R:131:2:
-! Arguments in `...` must be used.
-✖ Problematic argument:
-• ..1 = Inf
-ℹ Did you misspell an argument name?</code></pre>
-</div>
-<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>
-</h3>
-<pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">sce</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 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>class: SingleCellExperiment 
+dim: 29453 2411 
+metadata(0):
+assays(1): counts
+rownames(29453): ENSMUSG00000051951 ENSMUSG00000089699 ...
+  ENSMUSG00000095742 tomato-td
+rowData names(2): ENSEMBL SYMBOL
+colnames(2411): cell_9769 cell_9770 ... cell_12178 cell_12179
+colData names(11): cell barcode ... doub.density sizeFactor
+reducedDimNames(2): pca.corrected.E7.5 pca.corrected.E8.5
+mainExpName: NULL
+altExpNames(0):</code></pre>
 </div>
 <p>We can think of this (and other) class as a <em>container</em>, that
 contains several different pieces of data in so-called
@@ -335,27 +330,31 @@ <h2 id="the-assays">The <code>assays</code>
 <code>assay</code> function. If one of these matrices is called
 “counts”, we can use the special <code>counts</code> getter (and the
 analogous <code>logcounts</code>).</p>
-<div class="codewrapper sourceCode" id="cb6">
+<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>
 </h3>
 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu">identical</span><span class="op">(</span><span class="fu">assay</span><span class="op">(</span><span class="va">sce</span><span class="op">)</span>, <span class="fu">counts</span><span class="op">(</span><span class="va">sce</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 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 h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'assay': object 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>[1] TRUE</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb8">
+<div class="codewrapper sourceCode" id="cb6">
 <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">counts</span><span class="op">(</span><span class="va">sce</span><span class="op">)</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">3</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 h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'counts': object 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>3 x 3 sparse Matrix of class "dgTMatrix"
+                   cell_9769 cell_9770 cell_9771
+ENSMUSG00000051951         .         .         .
+ENSMUSG00000089699         .         .         .
+ENSMUSG00000102343         .         .         .</code></pre>
 </div>
 <p>You will notice that in this case we have a sparse matrix of class
 “dgTMatrix” inside the object. More generally, any “matrix-like” object
@@ -369,61 +368,142 @@ <h2 id="the-coldata-and-rowdata">The <code>colData</code> and <code>rowData</cod
 the rows of your assay, respectively.</p>
 <p>One can interact with them as usual, e.g., by extracting columns or
 adding additional variables as columns.</p>
-<div class="codewrapper sourceCode" id="cb10">
+<div class="codewrapper sourceCode" id="cb8">
 <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">colData</span><span class="op">(</span><span class="va">sce</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 h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colData': object 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>DataFrame with 2411 rows and 11 columns
+                  cell          barcode    sample       stage    tomato
+           &lt;character&gt;      &lt;character&gt; &lt;integer&gt; &lt;character&gt; &lt;logical&gt;
+cell_9769    cell_9769 AAACCTGAGACTGTAA         5        E8.5      TRUE
+cell_9770    cell_9770 AAACCTGAGATGCCTT         5        E8.5      TRUE
+cell_9771    cell_9771 AAACCTGAGCAGCCTC         5        E8.5      TRUE
+cell_9772    cell_9772 AAACCTGCATACTCTT         5        E8.5      TRUE
+cell_9773    cell_9773 AAACGGGTCAACACCA         5        E8.5      TRUE
+...                ...              ...       ...         ...       ...
+cell_12175  cell_12175 TTTGGTTAGTCCGTAT         5        E8.5      TRUE
+cell_12176  cell_12176 TTTGGTTAGTGTTGAA         5        E8.5      TRUE
+cell_12177  cell_12177 TTTGGTTGTTAAAGAC         5        E8.5      TRUE
+cell_12178  cell_12178 TTTGGTTTCAGTCAGT         5        E8.5      TRUE
+cell_12179  cell_12179 TTTGGTTTCGCCATAA         5        E8.5      TRUE
+                pool stage.mapped        celltype.mapped closest.cell
+           &lt;integer&gt;  &lt;character&gt;            &lt;character&gt;  &lt;character&gt;
+cell_9769          3        E8.25             Mesenchyme   cell_24159
+cell_9770          3         E8.5            Endothelium   cell_96660
+cell_9771          3         E8.5              Allantois  cell_134982
+cell_9772          3         E8.5             Erythroid3  cell_133892
+cell_9773          3        E8.25             Erythroid1   cell_76296
+...              ...          ...                    ...          ...
+cell_12175         3         E8.5             Erythroid3  cell_138060
+cell_12176         3         E8.5 Forebrain/Midbrain/H..   cell_72709
+cell_12177         3        E8.25       Surface ectoderm  cell_100275
+cell_12178         3        E8.25             Erythroid2   cell_70906
+cell_12179         3         E8.5            Spinal cord  cell_102334
+           doub.density sizeFactor
+              &lt;numeric&gt;  &lt;numeric&gt;
+cell_9769    0.02985045    1.41243
+cell_9770    0.00172753    1.22757
+cell_9771    0.01338013    1.15439
+cell_9772    0.00218402    1.28676
+cell_9773    0.00211723    1.78719
+...                 ...        ...
+cell_12175   0.00129403   1.219506
+cell_12176   0.01833074   1.095753
+cell_12177   0.03104037   0.910728
+cell_12178   0.00169483   2.061701
+cell_12179   0.03767894   1.798687</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb12">
+<div class="codewrapper sourceCode" id="cb10">
 <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">rowData</span><span class="op">(</span><span class="va">sce</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 h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'rowData': object 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>DataFrame with 29453 rows and 2 columns
+                              ENSEMBL         SYMBOL
+                          &lt;character&gt;    &lt;character&gt;
+ENSMUSG00000051951 ENSMUSG00000051951           Xkr4
+ENSMUSG00000089699 ENSMUSG00000089699         Gm1992
+ENSMUSG00000102343 ENSMUSG00000102343        Gm37381
+ENSMUSG00000025900 ENSMUSG00000025900            Rp1
+ENSMUSG00000025902 ENSMUSG00000025902          Sox17
+...                               ...            ...
+ENSMUSG00000095041 ENSMUSG00000095041     AC149090.1
+ENSMUSG00000063897 ENSMUSG00000063897          DHRSX
+ENSMUSG00000096730 ENSMUSG00000096730       Vmn2r122
+ENSMUSG00000095742 ENSMUSG00000095742 CAAA01147332.1
+tomato-td                   tomato-td      tomato-td</code></pre>
 </div>
 <p>Note the <code>$</code> short cut.</p>
-<div class="codewrapper sourceCode" id="cb14">
+<div class="codewrapper sourceCode" id="cb12">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu">identical</span><span class="op">(</span><span class="fu">colData</span><span class="op">(</span><span class="va">sce</span><span class="op">)</span><span class="op">$</span><span class="va">sum</span>, <span class="va">sce</span><span class="op">$</span><span class="va">sum</span><span class="op">)</span></span></code></pre>
 </div>
 <div class="codewrapper">
-<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="error" tabindex="0"><code>Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colData': object 'sce' not found</code></pre>
-</div>
-<div class="codewrapper sourceCode" id="cb16">
-<h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">sce</span><span class="op">$</span><span class="va">my_sum</span> <span class="op">&lt;-</span> <span class="fu">colSums</span><span class="op">(</span><span class="fu">counts</span><span class="op">(</span><span class="va">sce</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 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 h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colSums': error in evaluating the argument 'object' in selecting a method for function 'counts': object 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>[1] TRUE</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb18">
+<div class="codewrapper sourceCode" id="cb14">
 <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">colData</span><span class="op">(</span><span class="va">sce</span><span class="op">)</span></span></code></pre>
+<code class="sourceCode R"><span><span class="va">sce</span><span class="op">$</span><span class="va">my_sum</span> <span class="op">&lt;-</span> <span class="fu">colSums</span><span class="op">(</span><span class="fu">counts</span><span class="op">(</span><span class="va">sce</span><span class="op">)</span><span class="op">)</span></span>
+<span><span class="fu">colData</span><span class="op">(</span><span class="va">sce</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 h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colData': object 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>DataFrame with 2411 rows and 12 columns
+                  cell          barcode    sample       stage    tomato
+           &lt;character&gt;      &lt;character&gt; &lt;integer&gt; &lt;character&gt; &lt;logical&gt;
+cell_9769    cell_9769 AAACCTGAGACTGTAA         5        E8.5      TRUE
+cell_9770    cell_9770 AAACCTGAGATGCCTT         5        E8.5      TRUE
+cell_9771    cell_9771 AAACCTGAGCAGCCTC         5        E8.5      TRUE
+cell_9772    cell_9772 AAACCTGCATACTCTT         5        E8.5      TRUE
+cell_9773    cell_9773 AAACGGGTCAACACCA         5        E8.5      TRUE
+...                ...              ...       ...         ...       ...
+cell_12175  cell_12175 TTTGGTTAGTCCGTAT         5        E8.5      TRUE
+cell_12176  cell_12176 TTTGGTTAGTGTTGAA         5        E8.5      TRUE
+cell_12177  cell_12177 TTTGGTTGTTAAAGAC         5        E8.5      TRUE
+cell_12178  cell_12178 TTTGGTTTCAGTCAGT         5        E8.5      TRUE
+cell_12179  cell_12179 TTTGGTTTCGCCATAA         5        E8.5      TRUE
+                pool stage.mapped        celltype.mapped closest.cell
+           &lt;integer&gt;  &lt;character&gt;            &lt;character&gt;  &lt;character&gt;
+cell_9769          3        E8.25             Mesenchyme   cell_24159
+cell_9770          3         E8.5            Endothelium   cell_96660
+cell_9771          3         E8.5              Allantois  cell_134982
+cell_9772          3         E8.5             Erythroid3  cell_133892
+cell_9773          3        E8.25             Erythroid1   cell_76296
+...              ...          ...                    ...          ...
+cell_12175         3         E8.5             Erythroid3  cell_138060
+cell_12176         3         E8.5 Forebrain/Midbrain/H..   cell_72709
+cell_12177         3        E8.25       Surface ectoderm  cell_100275
+cell_12178         3        E8.25             Erythroid2   cell_70906
+cell_12179         3         E8.5            Spinal cord  cell_102334
+           doub.density sizeFactor    my_sum
+              &lt;numeric&gt;  &lt;numeric&gt; &lt;numeric&gt;
+cell_9769    0.02985045    1.41243     27577
+cell_9770    0.00172753    1.22757     29309
+cell_9771    0.01338013    1.15439     28795
+cell_9772    0.00218402    1.28676     34794
+cell_9773    0.00211723    1.78719     38300
+...                 ...        ...       ...
+cell_12175   0.00129403   1.219506     26680
+cell_12176   0.01833074   1.095753     19013
+cell_12177   0.03104037   0.910728     24627
+cell_12178   0.00169483   2.061701     46162
+cell_12179   0.03767894   1.798687     38398</code></pre>
 </div>
 </div>
 <div class="section level2">
@@ -436,16 +516,17 @@ <h2 id="the-reduceddims">The <code>reducedDims</code>
 <p>One of the peculiarity of SingleCellExperiment is its ability to
 store reduced dimension matrices within the object. These may include
 PCA, t-SNE, UMAP, etc.</p>
-<div class="codewrapper sourceCode" id="cb20">
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 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu">reducedDims</span><span class="op">(</span><span class="va">sce</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 h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'reducedDims': object 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>List of length 2
+names(2): pca.corrected.E7.5 pca.corrected.E8.5</code></pre>
 </div>
 <p>As for the other slots, we have the usual setter/getter, but it is
 somewhat rare to interact directly with these functions.</p>
@@ -457,7 +538,7 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 <em>indirectly</em> from the objects. Note that one could obtain the
 same results (somewhat less efficiently) by extracting the corresponding
 <code>reducedDim</code> matrix and <code>ggplot</code>.</p>
-<div class="codewrapper sourceCode" id="cb22">
+<div class="codewrapper sourceCode" id="cb18">
 <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">
@@ -473,18 +554,18 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>Loading required package: ggplot2</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb25">
+<div class="codewrapper sourceCode" id="cb21">
 <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">plotReducedDim</span><span class="op">(</span><span class="va">sce</span>, <span class="st">"pca.corrected.E8.5"</span>, colour_by <span class="op">=</span> <span class="st">"celltype.mapped"</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">WARNING<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 'reducedDim': object 'sce' not found</code></pre>
+<pre class="warning" tabindex="0"><code>Warning: Removed 131 rows containing missing values (`geom_point()`).</code></pre>
 </div>
-<div id="exercise-1" class="callout challenge">
+<figure><img src="../fig/intro-sce-rendered-unnamed-chunk-7-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><div id="exercise-1" class="callout challenge">
 <div class="callout-square">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
@@ -504,7 +585,7 @@ <h3 class="callout-title">Exercise 1<a class="anchor" aria-label="anchor" href="
 <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>SingleCellExperiment</code> function can be used to create
 a new SingleCellExperiment object</p>
@@ -517,7 +598,7 @@ <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="#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>TODO</p>
 </div>
@@ -545,7 +626,7 @@ <h3 class="callout-title">Exercise 2<a class="anchor" aria-label="anchor" href="
 <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>TODO</p>
 </div>
@@ -635,8 +716,8 @@ <h1 id="further-reading">Further Reading<a class="anchor" aria-label="anchor" hr
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/intro-sce.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/intro-sce.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-02-06",
-  "datePublished": "2024-02-06"
+  "dateModified": "2024-02-08",
+  "datePublished": "2024-02-08"
 }
 
   </script><script>
diff --git a/instructor/introduction.html b/instructor/introduction.html
index 446c5db..eb03cb5 100644
--- a/instructor/introduction.html
+++ b/instructor/introduction.html
@@ -233,7 +233,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Using RMarkdown</h1>
-        <p>Last updated on 2024-02-06 |
+        <p>Last updated on 2024-02-08 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/introduction.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -441,12 +441,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>Loading required package: SpatialExperiment</code></pre>
 </div>
-<div class="codewrapper">
-<h3 class="code-label">WARNING<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="warning" tabindex="0"><code>Warning: replacing previous import 'S4Arrays::makeNindexFromArrayViewport' by
-'DelayedArray::makeNindexFromArrayViewport' when loading 'HDF5Array'</code></pre>
-</div>
 <section id="introduction"><h2 class="section-heading">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
 <hr class="half-width"><p>This is a lesson created via The Carpentries Workbench. It is written
@@ -473,7 +467,7 @@ <h3 class="code-label">WARNING<i aria-hidden="true" data-feather="chevron-left">
   <h3 class="accordion-header" id="headingInstructor1">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="edit-2"></i></div>Instructor Note</h3>
 </button>
-<div id="collapseInstructor1" class="accordion-collapse collapse" data-bs-parent="#accordionInstructor1" aria-labelledby="headingInstructor1">
+<div id="collapseInstructor1" class="accordion-collapse collapse" aria-labelledby="headingInstructor1" data-bs-parent="#accordionInstructor1">
 <div class="accordion-body">
 <p>Inline instructor notes can help inform instructors of timing
 challenges associated with the lessons. They appear in the “Instructor
@@ -491,7 +485,7 @@ <h3 class="callout-title">Challenge 1: Can you do it?<a class="anchor" aria-labe
 </h3>
 <div class="callout-content">
 <p>What is the output of this command?</p>
-<div class="codewrapper sourceCode" id="cb27">
+<div class="codewrapper sourceCode" id="cb26">
 <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">
@@ -505,7 +499,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <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">Output</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">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -534,7 +528,7 @@ <h3 class="callout-title">Challenge 2: how do you nest solutions within
 <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 add a line with at least three colons and a
 <code>solution</code> tag.</p>
@@ -545,7 +539,7 @@ <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </section><section id="figures"><h2 class="section-heading">Figures<a class="anchor" aria-label="anchor" href="#figures"></a>
 </h2>
 <hr class="half-width"><p>You can also include figures generated from R Markdown:</p>
-<div class="codewrapper sourceCode" id="cb29">
+<div class="codewrapper sourceCode" id="cb28">
 <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">
@@ -665,8 +659,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/introduction.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/introduction.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-02-06",
-  "datePublished": "2024-02-06"
+  "dateModified": "2024-02-08",
+  "datePublished": "2024-02-08"
 }
 
   </script><script>
diff --git a/instructor/key-points.html b/instructor/key-points.html
index 444a486..9888344 100644
--- a/instructor/key-points.html
+++ b/instructor/key-points.html
@@ -321,8 +321,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/key-points.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/key-points.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-02-06",
-  "datePublished": "2024-02-06"
+  "dateModified": "2024-02-08",
+  "datePublished": "2024-02-08"
 }
 
   </script><script>
diff --git a/instructor/profiles.html b/instructor/profiles.html
index 75a9b81..c5910f5 100644
--- a/instructor/profiles.html
+++ b/instructor/profiles.html
@@ -257,8 +257,8 @@ <h1>Learner Profiles</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/profiles.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/profiles.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-02-06",
-  "datePublished": "2024-02-06"
+  "dateModified": "2024-02-08",
+  "datePublished": "2024-02-08"
 }
 
   </script><script>
diff --git a/instructor/reference.html b/instructor/reference.html
index 3725994..58167d9 100644
--- a/instructor/reference.html
+++ b/instructor/reference.html
@@ -220,7 +220,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Reference</h1>
-        <p>Last updated on 2024-02-06 |
+        <p>Last updated on 2024-02-08 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/learners/reference.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -298,8 +298,8 @@ <h1>Reference</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/reference.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/reference.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-02-06",
-  "datePublished": "2024-02-06"
+  "dateModified": "2024-02-08",
+  "datePublished": "2024-02-08"
 }
 
   </script><script>
diff --git a/intro-sce.html b/intro-sce.html
index e279401..e8d6470 100644
--- a/intro-sce.html
+++ b/intro-sce.html
@@ -224,7 +224,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Introduction to Bioconductor and the SingleCellExperiment class</h1>
-        <p>Last updated on 2024-02-06 |
+        <p>Last updated on 2024-02-08 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/intro-sce.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -288,29 +288,24 @@ <h1 id="the-singlecellexperiment-class">The <code>SingleCellExperiment</code> cl
 <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">sce</span> <span class="op">&lt;-</span> <span class="fu">WTChimeraData</span><span class="op">(</span>samples<span class="op">=</span><span class="fl">5</span><span class="op">)</span></span></code></pre>
+<code class="sourceCode R"><span><span class="va">sce</span> <span class="op">&lt;-</span> <span class="fu">WTChimeraData</span><span class="op">(</span>samples<span class="op">=</span><span class="fl">5</span><span class="op">)</span></span>
+<span><span class="va">sce</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 `collect()`:
-! Failed to collect lazy table.
-Caused by error in `db_collect()` at dbplyr/R/verb-compute.R:131:2:
-! Arguments in `...` must be used.
-✖ Problematic argument:
-• ..1 = Inf
-ℹ Did you misspell an argument name?</code></pre>
-</div>
-<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>
-</h3>
-<pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">sce</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 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>class: SingleCellExperiment 
+dim: 29453 2411 
+metadata(0):
+assays(1): counts
+rownames(29453): ENSMUSG00000051951 ENSMUSG00000089699 ...
+  ENSMUSG00000095742 tomato-td
+rowData names(2): ENSEMBL SYMBOL
+colnames(2411): cell_9769 cell_9770 ... cell_12178 cell_12179
+colData names(11): cell barcode ... doub.density sizeFactor
+reducedDimNames(2): pca.corrected.E7.5 pca.corrected.E8.5
+mainExpName: NULL
+altExpNames(0):</code></pre>
 </div>
 <p>We can think of this (and other) class as a <em>container</em>, that
 contains several different pieces of data in so-called
@@ -333,27 +328,31 @@ <h2 id="the-assays">The <code>assays</code>
 <code>assay</code> function. If one of these matrices is called
 “counts”, we can use the special <code>counts</code> getter (and the
 analogous <code>logcounts</code>).</p>
-<div class="codewrapper sourceCode" id="cb6">
+<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>
 </h3>
 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu">identical</span><span class="op">(</span><span class="fu">assay</span><span class="op">(</span><span class="va">sce</span><span class="op">)</span>, <span class="fu">counts</span><span class="op">(</span><span class="va">sce</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 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 h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'assay': object 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>[1] TRUE</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb8">
+<div class="codewrapper sourceCode" id="cb6">
 <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">counts</span><span class="op">(</span><span class="va">sce</span><span class="op">)</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">3</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 h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'counts': object 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>3 x 3 sparse Matrix of class "dgTMatrix"
+                   cell_9769 cell_9770 cell_9771
+ENSMUSG00000051951         .         .         .
+ENSMUSG00000089699         .         .         .
+ENSMUSG00000102343         .         .         .</code></pre>
 </div>
 <p>You will notice that in this case we have a sparse matrix of class
 “dgTMatrix” inside the object. More generally, any “matrix-like” object
@@ -367,61 +366,142 @@ <h2 id="the-coldata-and-rowdata">The <code>colData</code> and <code>rowData</cod
 the rows of your assay, respectively.</p>
 <p>One can interact with them as usual, e.g., by extracting columns or
 adding additional variables as columns.</p>
-<div class="codewrapper sourceCode" id="cb10">
+<div class="codewrapper sourceCode" id="cb8">
 <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">colData</span><span class="op">(</span><span class="va">sce</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 h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colData': object 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>DataFrame with 2411 rows and 11 columns
+                  cell          barcode    sample       stage    tomato
+           &lt;character&gt;      &lt;character&gt; &lt;integer&gt; &lt;character&gt; &lt;logical&gt;
+cell_9769    cell_9769 AAACCTGAGACTGTAA         5        E8.5      TRUE
+cell_9770    cell_9770 AAACCTGAGATGCCTT         5        E8.5      TRUE
+cell_9771    cell_9771 AAACCTGAGCAGCCTC         5        E8.5      TRUE
+cell_9772    cell_9772 AAACCTGCATACTCTT         5        E8.5      TRUE
+cell_9773    cell_9773 AAACGGGTCAACACCA         5        E8.5      TRUE
+...                ...              ...       ...         ...       ...
+cell_12175  cell_12175 TTTGGTTAGTCCGTAT         5        E8.5      TRUE
+cell_12176  cell_12176 TTTGGTTAGTGTTGAA         5        E8.5      TRUE
+cell_12177  cell_12177 TTTGGTTGTTAAAGAC         5        E8.5      TRUE
+cell_12178  cell_12178 TTTGGTTTCAGTCAGT         5        E8.5      TRUE
+cell_12179  cell_12179 TTTGGTTTCGCCATAA         5        E8.5      TRUE
+                pool stage.mapped        celltype.mapped closest.cell
+           &lt;integer&gt;  &lt;character&gt;            &lt;character&gt;  &lt;character&gt;
+cell_9769          3        E8.25             Mesenchyme   cell_24159
+cell_9770          3         E8.5            Endothelium   cell_96660
+cell_9771          3         E8.5              Allantois  cell_134982
+cell_9772          3         E8.5             Erythroid3  cell_133892
+cell_9773          3        E8.25             Erythroid1   cell_76296
+...              ...          ...                    ...          ...
+cell_12175         3         E8.5             Erythroid3  cell_138060
+cell_12176         3         E8.5 Forebrain/Midbrain/H..   cell_72709
+cell_12177         3        E8.25       Surface ectoderm  cell_100275
+cell_12178         3        E8.25             Erythroid2   cell_70906
+cell_12179         3         E8.5            Spinal cord  cell_102334
+           doub.density sizeFactor
+              &lt;numeric&gt;  &lt;numeric&gt;
+cell_9769    0.02985045    1.41243
+cell_9770    0.00172753    1.22757
+cell_9771    0.01338013    1.15439
+cell_9772    0.00218402    1.28676
+cell_9773    0.00211723    1.78719
+...                 ...        ...
+cell_12175   0.00129403   1.219506
+cell_12176   0.01833074   1.095753
+cell_12177   0.03104037   0.910728
+cell_12178   0.00169483   2.061701
+cell_12179   0.03767894   1.798687</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb12">
+<div class="codewrapper sourceCode" id="cb10">
 <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">rowData</span><span class="op">(</span><span class="va">sce</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 h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'rowData': object 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>DataFrame with 29453 rows and 2 columns
+                              ENSEMBL         SYMBOL
+                          &lt;character&gt;    &lt;character&gt;
+ENSMUSG00000051951 ENSMUSG00000051951           Xkr4
+ENSMUSG00000089699 ENSMUSG00000089699         Gm1992
+ENSMUSG00000102343 ENSMUSG00000102343        Gm37381
+ENSMUSG00000025900 ENSMUSG00000025900            Rp1
+ENSMUSG00000025902 ENSMUSG00000025902          Sox17
+...                               ...            ...
+ENSMUSG00000095041 ENSMUSG00000095041     AC149090.1
+ENSMUSG00000063897 ENSMUSG00000063897          DHRSX
+ENSMUSG00000096730 ENSMUSG00000096730       Vmn2r122
+ENSMUSG00000095742 ENSMUSG00000095742 CAAA01147332.1
+tomato-td                   tomato-td      tomato-td</code></pre>
 </div>
 <p>Note the <code>$</code> short cut.</p>
-<div class="codewrapper sourceCode" id="cb14">
+<div class="codewrapper sourceCode" id="cb12">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu">identical</span><span class="op">(</span><span class="fu">colData</span><span class="op">(</span><span class="va">sce</span><span class="op">)</span><span class="op">$</span><span class="va">sum</span>, <span class="va">sce</span><span class="op">$</span><span class="va">sum</span><span class="op">)</span></span></code></pre>
 </div>
 <div class="codewrapper">
-<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="error" tabindex="0"><code>Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colData': object 'sce' not found</code></pre>
-</div>
-<div class="codewrapper sourceCode" id="cb16">
-<h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">sce</span><span class="op">$</span><span class="va">my_sum</span> <span class="op">&lt;-</span> <span class="fu">colSums</span><span class="op">(</span><span class="fu">counts</span><span class="op">(</span><span class="va">sce</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 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 h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colSums': error in evaluating the argument 'object' in selecting a method for function 'counts': object 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>[1] TRUE</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb18">
+<div class="codewrapper sourceCode" id="cb14">
 <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">colData</span><span class="op">(</span><span class="va">sce</span><span class="op">)</span></span></code></pre>
+<code class="sourceCode R"><span><span class="va">sce</span><span class="op">$</span><span class="va">my_sum</span> <span class="op">&lt;-</span> <span class="fu">colSums</span><span class="op">(</span><span class="fu">counts</span><span class="op">(</span><span class="va">sce</span><span class="op">)</span><span class="op">)</span></span>
+<span><span class="fu">colData</span><span class="op">(</span><span class="va">sce</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 h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'colData': object 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>DataFrame with 2411 rows and 12 columns
+                  cell          barcode    sample       stage    tomato
+           &lt;character&gt;      &lt;character&gt; &lt;integer&gt; &lt;character&gt; &lt;logical&gt;
+cell_9769    cell_9769 AAACCTGAGACTGTAA         5        E8.5      TRUE
+cell_9770    cell_9770 AAACCTGAGATGCCTT         5        E8.5      TRUE
+cell_9771    cell_9771 AAACCTGAGCAGCCTC         5        E8.5      TRUE
+cell_9772    cell_9772 AAACCTGCATACTCTT         5        E8.5      TRUE
+cell_9773    cell_9773 AAACGGGTCAACACCA         5        E8.5      TRUE
+...                ...              ...       ...         ...       ...
+cell_12175  cell_12175 TTTGGTTAGTCCGTAT         5        E8.5      TRUE
+cell_12176  cell_12176 TTTGGTTAGTGTTGAA         5        E8.5      TRUE
+cell_12177  cell_12177 TTTGGTTGTTAAAGAC         5        E8.5      TRUE
+cell_12178  cell_12178 TTTGGTTTCAGTCAGT         5        E8.5      TRUE
+cell_12179  cell_12179 TTTGGTTTCGCCATAA         5        E8.5      TRUE
+                pool stage.mapped        celltype.mapped closest.cell
+           &lt;integer&gt;  &lt;character&gt;            &lt;character&gt;  &lt;character&gt;
+cell_9769          3        E8.25             Mesenchyme   cell_24159
+cell_9770          3         E8.5            Endothelium   cell_96660
+cell_9771          3         E8.5              Allantois  cell_134982
+cell_9772          3         E8.5             Erythroid3  cell_133892
+cell_9773          3        E8.25             Erythroid1   cell_76296
+...              ...          ...                    ...          ...
+cell_12175         3         E8.5             Erythroid3  cell_138060
+cell_12176         3         E8.5 Forebrain/Midbrain/H..   cell_72709
+cell_12177         3        E8.25       Surface ectoderm  cell_100275
+cell_12178         3        E8.25             Erythroid2   cell_70906
+cell_12179         3         E8.5            Spinal cord  cell_102334
+           doub.density sizeFactor    my_sum
+              &lt;numeric&gt;  &lt;numeric&gt; &lt;numeric&gt;
+cell_9769    0.02985045    1.41243     27577
+cell_9770    0.00172753    1.22757     29309
+cell_9771    0.01338013    1.15439     28795
+cell_9772    0.00218402    1.28676     34794
+cell_9773    0.00211723    1.78719     38300
+...                 ...        ...       ...
+cell_12175   0.00129403   1.219506     26680
+cell_12176   0.01833074   1.095753     19013
+cell_12177   0.03104037   0.910728     24627
+cell_12178   0.00169483   2.061701     46162
+cell_12179   0.03767894   1.798687     38398</code></pre>
 </div>
 </div>
 <div class="section level2">
@@ -434,16 +514,17 @@ <h2 id="the-reduceddims">The <code>reducedDims</code>
 <p>One of the peculiarity of SingleCellExperiment is its ability to
 store reduced dimension matrices within the object. These may include
 PCA, t-SNE, UMAP, etc.</p>
-<div class="codewrapper sourceCode" id="cb20">
+<div class="codewrapper sourceCode" id="cb16">
 <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">reducedDims</span><span class="op">(</span><span class="va">sce</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 h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'reducedDims': object 'sce' not found</code></pre>
+<pre class="output" tabindex="0"><code>List of length 2
+names(2): pca.corrected.E7.5 pca.corrected.E8.5</code></pre>
 </div>
 <p>As for the other slots, we have the usual setter/getter, but it is
 somewhat rare to interact directly with these functions.</p>
@@ -455,7 +536,7 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 <em>indirectly</em> from the objects. Note that one could obtain the
 same results (somewhat less efficiently) by extracting the corresponding
 <code>reducedDim</code> matrix and <code>ggplot</code>.</p>
-<div class="codewrapper sourceCode" id="cb22">
+<div class="codewrapper sourceCode" id="cb18">
 <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">
@@ -471,18 +552,18 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>Loading required package: ggplot2</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb25">
+<div class="codewrapper sourceCode" id="cb21">
 <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">plotReducedDim</span><span class="op">(</span><span class="va">sce</span>, <span class="st">"pca.corrected.E8.5"</span>, colour_by <span class="op">=</span> <span class="st">"celltype.mapped"</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">WARNING<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 'reducedDim': object 'sce' not found</code></pre>
+<pre class="warning" tabindex="0"><code>Warning: Removed 131 rows containing missing values (`geom_point()`).</code></pre>
 </div>
-<div id="exercise-1" class="callout challenge">
+<figure><img src="fig/intro-sce-rendered-unnamed-chunk-7-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><div id="exercise-1" class="callout challenge">
 <div class="callout-square">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
@@ -502,7 +583,7 @@ <h3 class="callout-title">Exercise 1<a class="anchor" aria-label="anchor" href="
 <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>SingleCellExperiment</code> function can be used to create
 a new SingleCellExperiment object</p>
@@ -515,7 +596,7 @@ <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="#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>TODO</p>
 </div>
@@ -543,7 +624,7 @@ <h3 class="callout-title">Exercise 2<a class="anchor" aria-label="anchor" href="
 <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>TODO</p>
 </div>
@@ -633,8 +714,8 @@ <h1 id="further-reading">Further Reading<a class="anchor" aria-label="anchor" hr
   "url": "https://ccb-hms.github.io/osca-carpentries/intro-sce.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/intro-sce.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-02-06",
-  "datePublished": "2024-02-06"
+  "dateModified": "2024-02-08",
+  "datePublished": "2024-02-08"
 }
 
   </script><script>
diff --git a/introduction.html b/introduction.html
index 6c8c059..439e0dd 100644
--- a/introduction.html
+++ b/introduction.html
@@ -233,7 +233,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Using RMarkdown</h1>
-        <p>Last updated on 2024-02-06 |
+        <p>Last updated on 2024-02-08 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/introduction.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -439,12 +439,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>Loading required package: SpatialExperiment</code></pre>
 </div>
-<div class="codewrapper">
-<h3 class="code-label">WARNING<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="warning" tabindex="0"><code>Warning: replacing previous import 'S4Arrays::makeNindexFromArrayViewport' by
-'DelayedArray::makeNindexFromArrayViewport' when loading 'HDF5Array'</code></pre>
-</div>
 <section id="introduction"><h2 class="section-heading">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
 <hr class="half-width"><p>This is a lesson created via The Carpentries Workbench. It is written
@@ -474,7 +468,7 @@ <h3 class="callout-title">Challenge 1: Can you do it?<a class="anchor" aria-labe
 </h3>
 <div class="callout-content">
 <p>What is the output of this command?</p>
-<div class="codewrapper sourceCode" id="cb27">
+<div class="codewrapper sourceCode" id="cb26">
 <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">
@@ -488,7 +482,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <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">Output</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">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -517,7 +511,7 @@ <h3 class="callout-title">Challenge 2: how do you nest solutions within
 <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 add a line with at least three colons and a
 <code>solution</code> tag.</p>
@@ -528,7 +522,7 @@ <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </section><section id="figures"><h2 class="section-heading">Figures<a class="anchor" aria-label="anchor" href="#figures"></a>
 </h2>
 <hr class="half-width"><p>You can also include figures generated from R Markdown:</p>
-<div class="codewrapper sourceCode" id="cb29">
+<div class="codewrapper sourceCode" id="cb28">
 <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">
@@ -648,8 +642,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://ccb-hms.github.io/osca-carpentries/introduction.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/introduction.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-02-06",
-  "datePublished": "2024-02-06"
+  "dateModified": "2024-02-08",
+  "datePublished": "2024-02-08"
 }
 
   </script><script>
diff --git a/key-points.html b/key-points.html
index 84c971b..47477bc 100644
--- a/key-points.html
+++ b/key-points.html
@@ -319,8 +319,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
   "url": "https://ccb-hms.github.io/osca-carpentries/key-points.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/key-points.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-02-06",
-  "datePublished": "2024-02-06"
+  "dateModified": "2024-02-08",
+  "datePublished": "2024-02-08"
 }
 
   </script><script>
diff --git a/md5sum.txt b/md5sum.txt
index 7508f04..96dea49 100644
--- a/md5sum.txt
+++ b/md5sum.txt
@@ -1,13 +1,13 @@
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-"CODE_OF_CONDUCT.md" "c93c83c630db2fe2462240bf72552548" "site/built/CODE_OF_CONDUCT.md" "2024-02-06"
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-"instructors/instructor-notes.md" "cae72b6712578d74a49fea7513099f8c" "site/built/instructor-notes.md" "2024-02-06"
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-"renv/profiles/lesson-requirements/renv.lock" "e36c766240cb3c98b81278f5337f6098" "site/built/renv.lock" "2024-02-06"
+"CODE_OF_CONDUCT.md" "c93c83c630db2fe2462240bf72552548" "site/built/CODE_OF_CONDUCT.md" "2024-02-08"
+"LICENSE.md" "b24ebbb41b14ca25cf6b8216dda83e5f" "site/built/LICENSE.md" "2024-02-08"
+"config.yaml" "c892677633a4fc1402d63fadc41c3980" "site/built/config.yaml" "2024-02-08"
+"index.md" "a02c9c785ed98ddd84fe3d34ddb12fcd" "site/built/index.md" "2024-02-08"
+"links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2024-02-08"
+"episodes/introduction.Rmd" "5d7045231f7b6e2f3e948745970f321b" "site/built/introduction.md" "2024-02-08"
+"episodes/intro-sce.Rmd" "63a3911b55029c417f64d98ebf3e4d49" "site/built/intro-sce.md" "2024-02-08"
+"instructors/instructor-notes.md" "cae72b6712578d74a49fea7513099f8c" "site/built/instructor-notes.md" "2024-02-08"
+"learners/reference.md" "1c7cc4e229304d9806a13f69ca1b8ba4" "site/built/reference.md" "2024-02-08"
+"learners/setup.md" "61568b36c8b96363218c9736f6aee03a" "site/built/setup.md" "2024-02-08"
+"profiles/learner-profiles.md" "60b93493cf1da06dfd63255d73854461" "site/built/learner-profiles.md" "2024-02-08"
+"renv/profiles/lesson-requirements/renv.lock" "70f621c14c52ece4187cf109419d4d03" "site/built/renv.lock" "2024-02-08"
diff --git a/pkgdown.yml b/pkgdown.yml
index 9243084..a40fc23 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 2.19.2
 pkgdown: 2.0.7
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-02-06T22:40Z
+last_built: 2024-02-08T23:01Z
 
diff --git a/profiles.html b/profiles.html
index 281f9b5..005cba3 100644
--- a/profiles.html
+++ b/profiles.html
@@ -257,8 +257,8 @@ <h1>Learner Profiles</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/profiles.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/profiles.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-02-06",
-  "datePublished": "2024-02-06"
+  "dateModified": "2024-02-08",
+  "datePublished": "2024-02-08"
 }
 
   </script><script>
diff --git a/reference.html b/reference.html
index e1c68c3..862e7cd 100644
--- a/reference.html
+++ b/reference.html
@@ -220,7 +220,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Reference</h1>
-        <p>Last updated on 2024-02-06 |
+        <p>Last updated on 2024-02-08 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/learners/reference.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -296,8 +296,8 @@ <h1>Reference</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/reference.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/reference.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-02-06",
-  "datePublished": "2024-02-06"
+  "dateModified": "2024-02-08",
+  "datePublished": "2024-02-08"
 }
 
   </script><script>