We used DESeq2 a lot at our research projects. Recently I was asked about specific experimental design for DESeq2.
We have 10 subjects that we will perform surgery on and measure mRNAs before surgery, during surgery, and 3 follow up time points.
All 10 subjects were collected at the pre, during, and the first follow up.
Only 7 were collect at the 2nd follow up and 6 were collected at the 3rd follow up.
This is a question of paired or unpaired analyses. We can perform a paired analysis for the “during” and “1st” follow up to the “pre”, but we don’t have a full paired set for the 2nd and 3rd follow up time points.
What do you recommendation for comparing 2nd follow up vs 1st follow up? Should we use all 10 samples in 1st follow up and 7 samples in 2nd follow up and set the patient ids as covariance even there are three patients existed at 1st follow up only? Or we have to use the 7 paired samples only?