I have a study design with 2 biological replicates where I want to know the differentially expressed genes in each of these across different time points.
I want to contrast state DIAGNOSIS to the other states for each sample. What should be my design? I have tried a couple of ways to do this, going through forums but could not arrive at a contrast for all states e.g. A_stateDiagnosis_vs_RELAPSE1, B_stateDiagnosis_vs_RELAPSE3 etc.