deploy: 7ce161e

day01.html

@@ -398,7 +398,7 @@
 
 <h1 class="title toc-ignore">DESeq2 Analysis with R: Part 01</h1>
 <h4 class="author">Thomas Manke @ MPI-IE</h4>
-<h4 class="date">Tue May 14 22:36:48 2024</h4>
+<h4 class="date">Tue May 14 23:57:01 2024</h4>
 
 </div>
 

day02.html

@@ -398,7 +398,7 @@
 
 <h1 class="title toc-ignore">DESeq2 Analysis with R: Part 02</h1>
 <h4 class="author">Bioinfo-Core @ MPI-IE</h4>
-<h4 class="date">Tue May 14 22:37:00 2024</h4>
+<h4 class="date">Tue May 14 23:57:13 2024</h4>
 
 </div>
 
@@ -780,19 +780,18 @@ <h3>Normalization and size factors</h3>
 <td align="left">sequencing depth and gene length</td>
 </tr>
 <tr class="odd">
-<td align="left">DESeq2 median of ratios</td>
+<td align="left">DESeq2 size factor</td>
 <td align="left">sequencing depth and RNA composition</td>
 </tr>
 </tbody>
 </table>
 <p>… and many others exist.</p>
 <p>DESeq2 Workflow for the ‘median of ratios’:</p>
-<ul>
-<li>Take geometric mean per gene (of all samples!) -&gt;
-‘pseudosample’</li>
-<li>calculate the count / pseudosample ratio</li>
-<li>‘sizefactor’ == median(ratios)</li>
-</ul>
+<div class="float">
+<img src="images/DESeq2_sizefactor.jpeg"
+alt="DESeq2 sizefactor determination." />
+<div class="figcaption">DESeq2 sizefactor determination.</div>
+</div>
 <blockquote>
 <p><strong>Task (5 min)</strong>: Plot a heatmap of the first 10 genes
 (rows) of the counts matrix and add the metadata after DESeq was run as
@@ -1123,10 +1122,10 @@ <h3>Model fit and testing</h3>
 <pre class="r"><code>dds_res %&gt;% 
   data.frame() %&gt;% 
   subset(padj &lt; 0.05) %&gt;% 
-  arrange(abs(log2FoldChange), descending=TRUE) %&gt;% head(20)</code></pre>
+  arrange(-abs(log2FoldChange)) %&gt;% head(20)</code></pre>
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day03.html

@@ -398,7 +398,7 @@
 
 <h1 class="title toc-ignore">DESeq2 Analysis with R: Part 03</h1>
 <h4 class="author">Bioinfo-Core @ MPI-IE</h4>
-<h4 class="date">Tue May 14 22:37:27 2024</h4>
+<h4 class="date">Tue May 14 23:57:39 2024</h4>
 
 </div>
 

day04.html

@@ -398,7 +398,7 @@
 
 <h1 class="title toc-ignore">deseq2 - applied</h1>
 <h4 class="author">Bioinfo-Core @ MPI-IE</h4>
-<h4 class="date">Tue May 14 22:40:02 2024</h4>
+<h4 class="date">Wed May 15 00:00:13 2024</h4>
 
 </div>
 

index.html

@@ -398,7 +398,7 @@
 
 <h1 class="title toc-ignore">DESeq2 Analysis with R: Description</h1>
 <h4 class="author">Bioinfo-Core @ MPI-IE</h4>
-<h4 class="date">Tue May 14 22:40:26 2024</h4>
+<h4 class="date">Wed May 15 00:00:37 2024</h4>
 
 </div>
 

outline.html

@@ -398,7 +398,7 @@
 
 <h1 class="title toc-ignore">DESeq2 Analysis with R: outline</h1>
 <h4 class="author">Bioinfo-Core @ MPI-IE</h4>
-<h4 class="date">Tue May 14 22:40:26 2024</h4>
+<h4 class="date">Wed May 15 00:00:37 2024</h4>
 
 </div>
 

summary.html

@@ -398,7 +398,7 @@
 
 <h1 class="title toc-ignore">DESeq2 Analysis with R: outline</h1>
 <h4 class="author">Bioinfo-Core @ MPI-IE</h4>
-<h4 class="date">Tue May 14 22:40:27 2024</h4>
+<h4 class="date">Wed May 15 00:00:37 2024</h4>
 
 </div>