I have 3 muscle types
I have 3 replicates between each and want to perform differential expression across all 3 to see which transcripts are being significantly differentially expressed. I have been using Cuffdiff because it's simple and the output is nice in that it has pairwise comparisons between everything.
I tried this with DESeq2, factor being muscle, level 1 being keel (select the 3 replicate count files), level 2 mantle, level 3 nuchal.
But when I ran the program and looked at the output it reported significance and expression values but it didn't tell me what samples it belonged to. I looked more into DESeq2 and it seems that the first level is accepted as the reference and then any further levels are just compared back to that. So I would have keel as the reference and then only get output of keel vs mantle, and keel vs nuchal. However I still don't know which is what since it doesn't tell me the samples it originates from. Additionally, I don't have a mantle vs nuchal comparison.
I'm assuming there's just something I am not understanding in the designing aspect of this setup. Can anyone give me some guidance?