I have RNASeq data from 4 groups with 3 biological replicates. The conditions are: 1) untreated, 2) treated with a drug, 3)infected with a virus, and 4) treated and infected. I am looking for DE genes unique for the treated and infected group (condition 4). I am wondering which model is the best for these data? I used "design <- model.matrix(~treatment + infection + treatment*infection)", but it is quite difficult to interpret.
Thanks in advance for any help.