Hello,

So, I have experiment design with 4 conditions, A, B, C, and D. I want to get the DE genes list with DESeq2 for all possible comparison (A-B,A-C,A-D,B-C,B-D,C-D). I tried voom/limma to do this and they can do it. Now, I want to try using DESeq2 to do this but apparently, most of the tutorial is only for 2 conditions. Is there any method to do this? I have specified conditions for design parameter in the DESeqDataSetFromMatrix. It only gave me the first and the last comparison (A-D). Anyone can help me? If it is not possible, what us the best way to do this?

Try reading the help page, specifically the contrast argument and see the Examples section, for the results function:

?results