Hi bioc-community, just for testing issue i have compared the output(diff. expr. genes) of limma and rank product. So I found, that with equal filtering parameters (fdr, foldchange), the intersection of genes that are assumed to be diff. expressed between both methods is between 60-70%. So although the approach of both methods is different, could it be imaginable to combine the output of both packages to increase the size of a gene set (so far regardless of stat. questions)? Has someone experience with that issue or experience with witch method provides more validity? best regards?, Georg