Beginner here - analyzing a RNA-seq dataset in Galaxy for differential expression. I've got a grip on everything except for analyzing the differential expression. I have three experimental groups of RNA from cultured cells:
- normal cells
- cells transfected with a negative control oligo
- cells transfected with an siRNA
Ideally I would like to normalize the expression of groups 2 and 3 to group 1, and then compare the expression of group 2 vs 3.
I can't figure out how to set up this kind of analysis in DESeq2 - is edgeR more appropriate? Set up each group and then set the contrast of interest to be 2 vs 3?
Thanks in advance!