I have some data from a collaborator which consists of p-values for ~2000 comparisons (proteins), and each protein was compared in several contrasts (control vs condition1, control vs condition2, etc).
When controlling for FDR in multiple comparisons one would input all the comparison p-values. However in this case would that mean:
- the p-values for all contrasts?
- or independently for each contrast?
The final goal of the analysis is to (i) find candidates in each comparison and (ii) determine the overlap of candidates between conditions.