add size factor illustration and update Wald test

maxplanck-ie · May 14, 2024 · 854276d · 854276d
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diff --git a/rmd/day02.Rmd b/rmd/day02.Rmd
@@ -285,16 +285,15 @@ A number of commonly used normalization techniques:
 |:-------|:-----|
 CPM | sequencing depth
 RPKM | sequencing depth and gene length
-DESeq2 median of ratios | sequencing depth and RNA composition
+DESeq2 size factor | sequencing depth and RNA composition
 
 ... and many others exist.
 
 
 DESeq2 Workflow for the 'median of ratios':
 
- * Take geometric mean per gene (of all samples!) -> 'pseudosample'
- * calculate the count / pseudosample ratio
- * 'sizefactor' == median(ratios) 
+![DESeq2 sizefactor determination.](images/DESeq2_sizefactor.jpeg)
+
 
 > **Task (5 min)**: Plot a heatmap of the first 10 genes (rows) of the counts matrix and add the metadata
 after DESeq was run as above.

diff --git a/rmd/images/DESeq2_sizefactor.jpeg b/rmd/images/DESeq2_sizefactor.jpeg
diff --git a/rmd/images/Wald_LRT.jpeg b/rmd/images/Wald_LRT.jpeg