I have RNA- Seq data from 7 samples with 4 different treatments(A,B,C,D) and one control(Z) (7samples X 5conditions). Now I want to use limma- voom to compute differentially expressed genes(up- regulated and down- regulated) across all four conditions. My question is how do I construct the model.matrix so that I can query genes that are up- regulated and down- regulated in all four conditions. I am not interested in pairwise comparisons, I am interested in genes that are differentially expressed in all four conditions(A,B,C,D vs Z).
Please throw some light on how to construct the model.matrix and contrast.fit.