updating 10 with pdf

Author: AbbiEdwards

Markdowns/10_DE_analysis_with_DESeq2_part1.Rmd

@@ -3,10 +3,10 @@ title: "Introduction to Bulk RNAseq data analysis"
 subtitle: Differential Expression of RNA-seq data - Part 1
 date: '`r format(Sys.time(), "Last modified: %d %b %Y")`'
 output:
-  html_document:
-    toc: yes
   pdf_document:
     toc: yes
+  html_document:
+    toc: yes
 bibliography: ref.bib
 ---
 
@@ -223,10 +223,11 @@ results.simple
 ### Exercise 1
 
 > Now we have made our results table using our simple model, let have a look at which
-> genes are changing and how many pass our 0.05 threshold. WHy might this not be
+> genes are changing and how many pass our 0.05 threshold. Why might this not be
 > straigtforward?
 >
 >
+
 ```{r echo=FALSE, message=FALSE, include=FALSE}
 sum(results.simple$padj < 0.05)
 ```
@@ -238,13 +239,15 @@ sum(is.na(results.simple$padj))
 > a) how many genes are significantly (with an FDR < 0.05) up-regulated?
 >
 >
+
 ```{r echo=FALSE, message=FALSE, include=FALSE}
 sum(results.simple$padj < 0.05 & results.simple$log2FoldChange > 0, na.rm = TRUE)
 ```
 >
 > b) how many genes are significantly (with an FDR < 0.05) down-regulated?
 >
 >
+
 ```{r echo=FALSE, message=FALSE, include=FALSE}
 sum(results.simple$padj < 0.05 & results.simple$log2FoldChange < 0, na.rm = TRUE)
 ```

Markdowns/10_DE_analysis_with_DESeq2_part1.html

@@ -187,7 +187,7 @@
 
 <h1 class="title toc-ignore">Introduction to Bulk RNAseq data analysis</h1>
 <h3 class="subtitle">Differential Expression of RNA-seq data - Part 1</h3>
-<h4 class="date">Last modified: 12 Nov 2021</h4>
+<h4 class="date">Last modified: 22 Nov 2021</h4>
 
 </div>
 
@@ -406,7 +406,7 @@ <h2>Generate a results table</h2>
 <div id="exercise-1" class="section level3">
 <h3>Exercise 1</h3>
 <blockquote>
-<p>Now we have made our results table using our simple model, let have a look at which genes are changing and how many pass our 0.05 threshold. WHy might this not be straigtforward?</p>
+<p>Now we have made our results table using our simple model, let have a look at which genes are changing and how many pass our 0.05 threshold. Why might this not be straigtforward?</p>
 </blockquote>
 <blockquote>
 <ol style="list-style-type: lower-alpha">