Hi everyone
I have patients RNA-seq data before and after treatment for one type of cancer. My goal is to use machine learning to predict drug response (response or resistance) and the treatment is one drug or two drugs. So, my question is what the best experimental design for Desq2 is:
One factor with 3 level: untreated (control) vs treated single drug vs treated double drugs
Two factors with 2 level: Factor 1: untreated (control) vs treated Factor 2: treated single drug vs treated double drugs
So in DESeq2, what is the main difference between one factor with 3 levels and two factors with two levels?