DESeq2 Factor Level Design

deseq2

#1

I have 3 muscles I am trying to perform differential expression with.

For each muscle type, I have 3 replicates.

How can I get pairwise comparisons between muscle 1 vs muscle 2, muscle 1 vs muscle 3, muscle 2 vs muscle 3. Within the DESeq2 tool I have factor set to muscle, then level 1 as muscle 1, level 2 and muscle 2, etc. Then within each level/,muscle type, I select the three replicate data count files.

I read that DESeq2 takes the first input as the reference (so that would be muscle 1) and then compares everything to that. But that’s not necessarily what I want. I have been using Cuffdiff to perform analyses but wanted to use a more updated tool but I can’t seem to set it up as it needs to be. Can anyone give me some guidance?