Hello, I have some questions about GOHyperG: After performing GOHyperG test: > test1<-GOHyperG(listSAM1) I would like to obtain a table of GO-ids and description and p-value of the first 10 GO-ids with lowest p-value. How can I do this? Does someone know wheter GOHyperG corrects for multiple testing? Best regards, Katleen -- *dr. ir. Katleen De Preter* Center for Medical Genetics Ghent (CMGG) Ghent University Hospital Medical Research Building (MRB), 2nd floor, room 120.038 De Pintelaan 185, B-9000 Ghent, Belgium +32 9 240 5533 (phone) | +32 9 240 6549 (fax) http://medgen.ugent.be Katleen.DePreter@UGent.be <mailto:katleen.depreter@ugent.be> -- No virus found in this outgoing message. Checked by AVG Anti-Virus.

On Feb 1, 2005, at 5:45 AM, Katleen De Preter wrote: > Hello, > I have some questions about GOHyperG: > After performing GOHyperG test: > > test1<-GOHyperG(listSAM1) > I would like to obtain a table of GO-ids and description and p-value > of the first 10 GO-ids with lowest p-value. > How can I do this? The vignette is somewhat helpful in this regard, as is the manual page. So, if you run the example, sort(xx$pvalues)[1:10] seems like a start. > Does someone know wheter GOHyperG corrects for multiple testing? Umm, well the manual page is pretty explicit, I can only recommend that you read it. There are no corrections made, you can make what ever ones you feel are appropriate, I personally know of no method that I would use or endorse for this situation. Robert > Best regards, > Katleen > > > > -- > *dr. ir. Katleen De Preter* > Center for Medical Genetics Ghent (CMGG) > Ghent University Hospital > Medical Research Building (MRB), 2nd floor, room 120.038 > De Pintelaan 185, B-9000 Ghent, Belgium > +32 9 240 5533 (phone) | +32 9 240 6549 (fax) > http://medgen.ugent.be > Katleen.DePreter@UGent.be <mailto:katleen.depreter@ugent.be> > > > -- > No virus found in this outgoing message. > Checked by AVG Anti-Virus. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > +--------------------------------------------------------------------- -- ----------------+ | Robert Gentleman phone: (206) 667-7700 | | Head, Program in Computational Biology fax: (206) 667-1319 | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center | | email: rgentlem@fhcrc.org | +--------------------------------------------------------------------- -- ----------------+