In my differential expression analysis dataset (comparing promotes of healthy cells vs diseased cells of patients with defined genotypes) I have a few genotypes with only 2 samples instead of the classically used 3.
To give it a try I included them in the makeContrast for LIMMA and it runs without complain. Also, if I check for proteins I would expect to be lower expressed like the ones mutated in the patients, they are significant in those groups (and even specifically in those groups only).
So my question is if this approach is ok and valid or a total NO GO that won't be accepted by any reviewer.
Thanks for your comments! Sebastian