Hello, I'm analyzing some RNA-Seq data using DESeq2 and have a couple of questions on how to set up my experimental design.
My experimental design has a control ("ctrl") and three treatments ("treat1", "treat2" and "treat3"). I want to see if there is an expression differences of these treatments compared to control.
Could anybody help me to write the contrast code? Also, can I run all the comparisons together or each treatment have to be compared separately to control?
res <- results(dds, contrast=c("treatment","ctrl","treat1",....))???