I have RNA-seq data (5 subjects are measured on 4 time points) and would like to do a SVA first to be able to include potential confounders into the statistical model (Deseq2 pipeline).
I am having troubles how to define my null and full model in the SVA:
Full model ~ TIME + SUBJECT.ID
Null model ~ SUBJECT.ID OR Null model ~ 1
Should the subjects ID be treated as a factor of interest or as a confounding factor?
Thanks in advance!