I have 3 groups in a RNASeq Experiment - A, B and C. Within each of these groups, I also have two genotypes, WT and KO.
I've run DESeq to determine differences among groups (without looking at genotypes yet).
Now, I know if I subset the DESeq object to contain only A and B groups, the sizefactors will remain the same as the full object (unless I re-run
estimatesizefactors() again). But, what about the dispersions? Will the dispersions estimations of the subset object be the same as the full object?
The main idea of subsetting A and B is that group C is quiet different from these two and wanted to check if having C or not could somehow influence the dispersion estimates.