Hi, Jim is right, but we should split out the different parts, all that the chip is used for is to define the universe and it is perfectly reasonable to want to define your own universe. Look for some changes in the devel arm later this week. One problem with that approach is that we will have no way to test that your Entrez Gene IDs are valid, so that is going to require that the user take all responsibility on that front (and it could have a big effect if you accidently add in a bunch of non-Entrez gene ids). best wishes Robert James W. MacDonald wrote: > knaxerov at ix.urz.uni-heidelberg.de wrote: > >>Hello everyone, >> >>here's a really trivial question, but I can't find the answer anywhere: can I >>use GOHyperG() in GOstats without specifying a particular microarray chip? I'd >>simply like to pass a list of EntrezGene IDs as my "total population". > > > No, GOHyperG() requires an annotation package to extract all the GO IDs > for each probe on the chip. > > Although it is a non-trivial task, you might consider building an > annotation package based on your vector of Entrez Gene IDs. This can > substantially simplify further annotation of results from your > microarray data. > > Best, > > Jim > > > >>Thanks!!!! >>Kamila >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor at stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor > > > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org