I have the following two questions, I would highly appreciate your input on both of these.
1) How to create a design matrix for a time point comparison where the patients were on and off treatment using DeSeq2? The patients were initially on drugA for a month and then off drugA for another month, the RNA was collected before the drug intake and a month after stoping the drug.
My phenotype file for the analysis looks this:
SampleName SampleID Condition
P1T1 Patient1 DrugA
P2T1 Patient1 DrugA
P3T1 Patient2 DrugA
P4T1 Patient2 DrugA
P1T2 Patient1 Off-A
P2T2 Patient1 Off-A
P3T2 Patient2 Off-A
P4T2 Patient2 Off-A
Here: P1T1 stands for Patient1 and time1(on DrugA) and P1T2 Patient1 and time2(Off-A). I have more patients but for this example I am just showing two patients with two replicates and two time points. (Here P*T* are columns of my expression matrix).
Can you please suggest a DeSeq2 design matrix for this?
2) Since the same patients were sequenced twice for both time points as technical replicates, does it make sense to combine the two replicates into one or consider them as two separate samples?
Please let me know if the post requires more explanation?