Hi Lola, It's hard to say what is going on with the little amount that you have told us. A sessionInfo() call is usually informative, along with code snippets to illustrate what you are trying to do. But based just on this thread, I see you trying to use probeSetSummary() with an org package (org.Mm.eg.db). And that doesn't really make too much sense, because the org package will not have any probes. I wonder if maybe what you meant to use was summary() instead? Or maybe you really should have used an annotation package that has probes in it? Perhaps one that matches the platform you are using (whatever that is)? Marc On 03/22/2012 09:05 AM, Lola Guerrero wrote: > Hi Jim, > > > > Thanks for your proposal, as you thought IâEUR^(TM)m using GOstats package (Agilent for > mouse). > > I was trying to figure out how to use probeSetSummary function and I found the > following error: > > > > probeSetSummary(myhyperGTest) > > > > Error en get(mapName, envir = pkgEnv, inherits = FALSE) : > > Object 'org.Mm.egENTREZID' not found > > > > So I need to check my code and find out where the problem is. Do you have any > advice? > > > > Thanks, > > > > Lola. > > > El 22 de marzo de 2012 a las 14:15 "James W. MacDonald"<jmacdon@uw.edu> > escribió: > >> Hi Lola, >> >> On 3/22/2012 8:33 AM, Lola Guerrero wrote: >>> Dear all, >>> >>> >>> >>> I have run a Hypergeometric test and so far so good. Now I am interested in >>> the >>> gene set that belong to a particular ontology. Do you know if exist any way >>> to >>> access to these genes? I mean, if for example I have an ontology which is >>> defined by 10 genes and in my case the test count 5, how can I access to >>> these >>> genes? >> It depends on what package you used. If you used the GOstats package, >> then there is probeSetSummary(). >> >> Best, >> >> Jim >> >> >>> >>> >>> Iââ,¬â"¢ll appreciate any help! Thank you very much for your help! >>> >>> >>> >>> Lola Guerrero >>> >>> >>> [[alternative HTML version deleted]] >>> >>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> -- >> James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >> > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]