I am trying to analyze a gene expression dataset with three treatments (A, B, and control). There should not be any interaction effect. I will be thankful to you if can briefly explain how to obtain differentially expressed genes under these conditions.
How can I define my reference for the expression analysis when I have three treatments? How can I define my formula?
is it ~ A + B?
when I show over-expressed genes, should I have two lists? e.g.,
A vs Control B vs Control