Dear list, I would like to ask on the theory behind various methods in decideTests. The method "separate" is clear to me, giving p-value adjustment for each contrast separately. The method "global" may be used presumably when there are two or more contrasts of similar strength in the experiment. The method "nestedF" seems to me similar to the "global", yet it considers for p-value adjustment only those genes for which F-test is significant after p-value correction (roughly said). Is that correct? And finally, the method "hierarchical" considers for the final p-value adjustment only those genes/contrasts for which adjusted p-value (of the gene in the contrast treated separately) is smaller than some cut-off. Is that right? My next question is whether any of the methods "global", "hierarchical" or "nestedF" can be used to correct p-values for contrasts that have different strength (different number of expected DEGs)? In my case 'different' means hundreds of DEGs for one contrast and tens for the other. Can I find more details on the methods in some reference? Cheers, Michal -- ----------------------------------------------------- Michal Kol?? Academy of Sciences of the Czech Republic Institute of Molecular Genetics