I've been reading up on corrections after DESeq2 and talking to other bioinformaticians and they say that you should adjust for all the comparisons that you made after running DESeq2, or adjust within each comparison. And DESeq2 automatically includes the adjusted p-values that account for multiple comparisons.
My question is this, how do we adjust the comparisons for either case?
Some examples would be much appreciated.
Thanks for any help provided.