Alex hi, I'm not sure whether you can directly prevent the hyperGTest function from testing small gene-sets. It tests all gene-sets as a default. However, you can certainly filter the list of significant gene-sets by set size. The summary() function for the test output has a "categorySize" argument. Suppose the output of your test is called "testresults". Then do: summary(testresults, categorySize=3) to filter out sets of 2 or less genes. My gut feeling is that you won't get significant gene-sets with 2 genes anyway, so to see any appreciable change in your results you'll have to set the threshold higher. The smallest significant set in the vignette example has 7 genes (6 of them marked as significant). Additionally, the summary function itself returns a data frame, one of whose column is "Size", so you can always arrange and filter the gene-set list later as well. Hope this helps, cheers, Assaf