diff --git a/rmd/day02.Rmd b/rmd/day02.Rmd index 14a8f8c..6e2b0b7 100644 --- 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 new file mode 100644 index 0000000..ef59a3d Binary files /dev/null and b/rmd/images/DESeq2_sizefactor.jpeg differ diff --git a/rmd/images/Wald_LRT.jpeg b/rmd/images/Wald_LRT.jpeg index 1bc1763..beb4621 100644 Binary files a/rmd/images/Wald_LRT.jpeg and b/rmd/images/Wald_LRT.jpeg differ