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carpentries-incubator · Apr 4, 2024 · 1ed3475 · 1ed3475
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diff --git a/_episodes/04-principal-component-analysis.md b/_episodes/04-principal-component-analysis.md
@@ -810,8 +810,8 @@ represents.
 > > 215281_x_at 0.003923775 0.003179556 -0.0004388192 9.664648e-05 0.003501335
 > >                    PC86        PC87          PC88         PC89         PC90
 > > 215281_x_at -0.00112973 0.006489667 -0.0005039785 -0.004296355 -0.002751513
-> >                     PC91
-> > 215281_x_at -0.002231113
+> >                    PC91
+> > 215281_x_at -0.00383085
 > > ~~~
 > > {: .output}
 > > 
@@ -876,7 +876,7 @@ represents.
 > >                    PC82        PC83         PC84       PC85       PC86
 > > 211122_s_at -0.01988441 0.009667348 -0.008248781 0.01198369 0.01221713
 > >                     PC87        PC88        PC89        PC90        PC91
-> > 211122_s_at -0.003864842 -0.02876816 -0.01771452 -0.02164973 0.003856584
+> > 211122_s_at -0.003864842 -0.02876816 -0.01771452 -0.02164973 0.004593411
 > > ~~~
 > > {: .output}
 > > The function `pca()` is used to perform PCA, and uses as input a matrix

diff --git a/fig/rmd-01-pairs-prostate-1.png b/fig/rmd-01-pairs-prostate-1.png
diff --git a/fig/rmd-02-example1-1.png b/fig/rmd-02-example1-1.png
diff --git a/fig/rmd-02-example2-1.png b/fig/rmd-02-example2-1.png
diff --git a/fig/rmd-02-example3-1.png b/fig/rmd-02-example3-1.png
diff --git a/fig/rmd-02-heatmap-1.png b/fig/rmd-02-heatmap-1.png
diff --git a/fig/rmd-02-histx-1.png b/fig/rmd-02-histx-1.png
diff --git a/fig/rmd-02-limmavolc1-1.png b/fig/rmd-02-limmavolc1-1.png
diff --git a/fig/rmd-02-limmavolc2-1.png b/fig/rmd-02-limmavolc2-1.png
diff --git a/fig/rmd-02-p-fdr-1.png b/fig/rmd-02-p-fdr-1.png
diff --git a/fig/rmd-02-p-fwer-1.png b/fig/rmd-02-p-fwer-1.png
diff --git a/fig/rmd-02-plot-fdr-fwer-1.png b/fig/rmd-02-plot-fdr-fwer-1.png
diff --git a/fig/rmd-02-plot-limma-lm-effect-1.png b/fig/rmd-02-plot-limma-lm-effect-1.png
diff --git a/fig/rmd-02-plot-limma-lm-pval-1.png b/fig/rmd-02-plot-limma-lm-pval-1.png
diff --git a/fig/rmd-02-plot-lm-methyl1-1.png b/fig/rmd-02-plot-lm-methyl1-1.png
diff --git a/fig/rmd-02-tdist-1.png b/fig/rmd-02-tdist-1.png
diff --git a/fig/rmd-02-volcplotfake-1.png b/fig/rmd-02-volcplotfake-1.png
diff --git a/fig/rmd-03-binomial-1.png b/fig/rmd-03-binomial-1.png
diff --git a/fig/rmd-03-chooselambda-1.png b/fig/rmd-03-chooselambda-1.png
diff --git a/fig/rmd-03-corr-mat-meth-1.png b/fig/rmd-03-corr-mat-meth-1.png
diff --git a/fig/rmd-03-elastic-1.png b/fig/rmd-03-elastic-1.png
diff --git a/fig/rmd-03-elastic-contour-1.png b/fig/rmd-03-elastic-contour-1.png
diff --git a/fig/rmd-03-elastic-cv-1.png b/fig/rmd-03-elastic-cv-1.png
diff --git a/fig/rmd-03-lasso-cv-1.png b/fig/rmd-03-lasso-cv-1.png
diff --git a/fig/rmd-03-plot-ridge-1.png b/fig/rmd-03-plot-ridge-1.png
diff --git a/fig/rmd-03-plot-ridge-prediction-1.png b/fig/rmd-03-plot-ridge-prediction-1.png
diff --git a/fig/rmd-03-plotlas-1.png b/fig/rmd-03-plotlas-1.png
diff --git a/fig/rmd-03-regplot-1.png b/fig/rmd-03-regplot-1.png
diff --git a/fig/rmd-03-ridgeplot-1.png b/fig/rmd-03-ridgeplot-1.png
diff --git a/fig/rmd-03-shrink-lasso-1.png b/fig/rmd-03-shrink-lasso-1.png
diff --git a/fig/rmd-03-test-plot-lm-1.png b/fig/rmd-03-test-plot-lm-1.png
diff --git a/fig/rmd-05-biplot-ex-1.png b/fig/rmd-05-biplot-ex-1.png
diff --git a/fig/rmd-05-loadingsplots-1.png b/fig/rmd-05-loadingsplots-1.png
diff --git a/fig/rmd-05-loadingsplots-2.png b/fig/rmd-05-loadingsplots-2.png
diff --git a/fig/rmd-05-loadingsplots-3.png b/fig/rmd-05-loadingsplots-3.png
diff --git a/fig/rmd-05-pairsplot-1.png b/fig/rmd-05-pairsplot-1.png
diff --git a/fig/rmd-05-pca-biplot-ex2-1.png b/fig/rmd-05-pca-biplot-ex2-1.png
diff --git a/fig/rmd-05-pca-by-hand-1.png b/fig/rmd-05-pca-by-hand-1.png
diff --git a/fig/rmd-05-pros-pcs-1.png b/fig/rmd-05-pros-pcs-1.png
diff --git a/fig/rmd-05-scree-ex-1.png b/fig/rmd-05-scree-ex-1.png
diff --git a/fig/rmd-05-stats-biplot-1.png b/fig/rmd-05-stats-biplot-1.png
diff --git a/fig/rmd-05-var-hist-1.png b/fig/rmd-05-var-hist-1.png
diff --git a/fig/rmd-05-varexp-1.png b/fig/rmd-05-varexp-1.png
diff --git a/fig/rmd-06-biplot-1.png b/fig/rmd-06-biplot-1.png
diff --git a/fig/rmd-08-boots-1.png b/fig/rmd-08-boots-1.png
diff --git a/fig/rmd-08-bs-ex-1.png b/fig/rmd-08-bs-ex-1.png
diff --git a/fig/rmd-08-bs-heatmap-1.png b/fig/rmd-08-bs-heatmap-1.png
diff --git a/fig/rmd-08-fake-cluster-1.png b/fig/rmd-08-fake-cluster-1.png
diff --git a/fig/rmd-08-kmeans-1.png b/fig/rmd-08-kmeans-1.png
diff --git a/fig/rmd-08-kmeans-ex-1.png b/fig/rmd-08-kmeans-ex-1.png
diff --git a/fig/rmd-08-plot-silhouette-1.png b/fig/rmd-08-plot-silhouette-1.png
diff --git a/fig/rmd-08-silhouette-1.png b/fig/rmd-08-silhouette-1.png
diff --git a/fig/rmd-08-silhouette-ex-1.png b/fig/rmd-08-silhouette-ex-1.png
diff --git a/fig/rmd-08-unnamed-chunk-1-1.png b/fig/rmd-08-unnamed-chunk-1-1.png
diff --git a/fig/rmd-08-unnamed-chunk-2-1.png b/fig/rmd-08-unnamed-chunk-2-1.png
diff --git a/fig/rmd-09-clust-cor-cor-example-1.png b/fig/rmd-09-clust-cor-cor-example-1.png
diff --git a/fig/rmd-09-clust-euc-cor-example-1.png b/fig/rmd-09-clust-euc-cor-example-1.png
diff --git a/fig/rmd-09-cresClustDefault-1.png b/fig/rmd-09-cresClustDefault-1.png
diff --git a/fig/rmd-09-crescents-1.png b/fig/rmd-09-crescents-1.png
diff --git a/fig/rmd-09-cutree-1.png b/fig/rmd-09-cutree-1.png
diff --git a/fig/rmd-09-h-k-ex-plot-1.png b/fig/rmd-09-h-k-ex-plot-1.png
diff --git a/fig/rmd-09-hclust-fig3-1.png b/fig/rmd-09-hclust-fig3-1.png
diff --git a/fig/rmd-09-hclust-fig4-1.png b/fig/rmd-09-hclust-fig4-1.png
diff --git a/fig/rmd-09-heatmap-clust-1.png b/fig/rmd-09-heatmap-clust-1.png
diff --git a/fig/rmd-09-heatmap-cor-cor-example-1.png b/fig/rmd-09-heatmap-cor-cor-example-1.png
diff --git a/fig/rmd-09-heatmap-cor-cor-example-2.png b/fig/rmd-09-heatmap-cor-cor-example-2.png
diff --git a/fig/rmd-09-heatmap-cor-example-1.png b/fig/rmd-09-heatmap-cor-example-1.png
diff --git a/fig/rmd-09-heatmap-noclust-1.png b/fig/rmd-09-heatmap-noclust-1.png
diff --git a/fig/rmd-09-lineplot-cor-example-1.png b/fig/rmd-09-lineplot-cor-example-1.png
diff --git a/fig/rmd-09-plot-clust-average-1.png b/fig/rmd-09-plot-clust-average-1.png
diff --git a/fig/rmd-09-plot-clust-centroid-1.png b/fig/rmd-09-plot-clust-centroid-1.png
diff --git a/fig/rmd-09-plot-clust-comp-1.png b/fig/rmd-09-plot-clust-comp-1.png
diff --git a/fig/rmd-09-plot-clust-dunn-1.png b/fig/rmd-09-plot-clust-dunn-1.png
diff --git a/fig/rmd-09-plot-clust-mcq-1.png b/fig/rmd-09-plot-clust-mcq-1.png
diff --git a/fig/rmd-09-plot-clust-median-1.png b/fig/rmd-09-plot-clust-median-1.png
diff --git a/fig/rmd-09-plot-clust-method-1.png b/fig/rmd-09-plot-clust-method-1.png
diff --git a/fig/rmd-09-plot-clust-wardD-1.png b/fig/rmd-09-plot-clust-wardD-1.png
diff --git a/fig/rmd-09-plot-clust-wardD2-1.png b/fig/rmd-09-plot-clust-wardD2-1.png
diff --git a/fig/rmd-09-plot-clusters-1.png b/fig/rmd-09-plot-clusters-1.png
diff --git a/fig/rmd-09-plot-coloured-branches-1.png b/fig/rmd-09-plot-coloured-branches-1.png
diff --git a/fig/rmd-09-plotclustex-1.png b/fig/rmd-09-plotclustex-1.png
diff --git a/fig/rmd-09-plotexample-1.png b/fig/rmd-09-plotexample-1.png