I am working on a set of RNAseq data that has the following design:
patients are randomized to different treatment groups: control, trt1 and trt2 each patient has pre and post treatment RNAseq data: time0 , time1
I am interested in getting treatment effect (not time effect). The model mentioned in DESeq2, edgeR and Limma helps to get time effect which is not the interest.
Any suggestion how to get treatment effect for RNAseq data with this design?
Thank you very much!