Dear Bioconductors,  

I recently used GSVA to get enrichment scores for three gene sets and four sample groups. From the enrichment scores, I am interested in determining if they are differentially expressed across several sample groups. I intend to do many sets of comparisons and thus I was planning to create separate contrast matrices for each set of comparisons. However, I am wondering if it is incorrect to break up these comparisons into separate matrices and if I instead should combine all comparisons for the study into one contrast matrix. Further, though I have used the Benjamini-Hochberg procedure for multiple comparisons, I think I have what is considered planned comparisons (i.e. only a few sensible comparisons which were decided before looking at the data). As such, is it incorrect to use the BH method or would you recommend using Bonferroni corretion? 

Thanks,

SB