Dear List, I looked through the archives and didn't notice anyone pointing this out, so I thought I'd ask: If decideTests() is called with the method argument set to hierarchical (by the way, that word is misspelled in the implementation as 'heirarchical' - if someone should call it with correct spelling, they get an error), then internally classifyTestsP() is called to adjust across contrasts (after adjusting across genes). So far so good (exc the spelling). However, it seems the multiple adjustment method is not propagated to classifyTestsP - so if the user requests adjust.method="BH", classifyTestsP will perform the default adjustment, "holm", which is more conservative. Is that behavior by design? Or is there just a "method=adjust.method" missing on the classifyTestsP() call? Also one could do fewer computations in the code, perhaps, if one did something like padj = p.adjust(object$F.p.value, method=adjust.method) sel = padj < 0.05 pmax=min(padj[!sel], na.rm=TRUE) results=classifyTestsP(object[sel,], p.value=pmax, method=adjust.method) for the hierarchical and nestedF branches of decideTests() - this avoids computing i, n, and a there. Or are these computed there for a reason, again? Thanks, --Misha K.