Hoping for some help. I can't seem to wrap my brain around how I should set up my design in DESeq2. Here are the details, I have 6 samples from each patients. I have two patients. Each sample represents a different timepoint of treatment. For each patient I have 2 age-matched healthy controls. So I have 8 samples that correspond to patient 1 and 8 samples that correspond to patient 2. We want to do two things:
1-Identify any DE miRNAs within a patient as a result of the treatment over time.
2-Identfify any DE miRNAs between patients at any of the time points.
I'm also really not sure of how to incoroporate the controls. Any help is greatly appreciated.