Question: DESeq2 with multiple conditions
1
3.8 years ago by
bharata180340
Japan
bharata180340 wrote:

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?

rnaseq deseq2 • 2.6k views
modified 3.8 years ago by Michael Love25k • written 3.8 years ago by bharata180340
1
3.8 years ago by
Michael Love25k
United States
Michael Love25k wrote:

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

?results