Hi Dick, The problem you mention is because topGO is using the old version of the GO package, the one based on environments and the GOstats is using the new GO.db package. The problem is that when you load GOstats, after topGO is loaded, the GO.db will load on top of the GO, on the search path. Then, every time topGO needs to access to the "functions" from the GO package it will access the ones from GO.db. And there are some incompatibilities between this two packages. The next release of the topGO will be based on the newly GO.db library. However, if you want to use the both packages, here is a quick hack: ## when switching from GOstats to topGO > detach(package:GO) > library(GO) ## when switching from topGO to GOstats > detach(package:GO.db) > library(GO.db) In this way, you know which GO package are you using at the moment. Sorry for the inconvenience. Adrian