Thank you for your answer, however I want the program automatically add a column to my table with the gene symbols that correspond to the most significant GO terms? So I don't want to do it for every GO manually. Best regards, Katleen Robert Gentleman wrote: > If what you want is the mapping from some manufacturer's identifiers > to gene symbols (?) then > you need to use the data packages (if you are using affy then you get > the one for your chip, if not, then you have more work to do, but you > didn't really give us very much to go on here) > > So, for example, if I had some affy ids from a HG-U95a2 chip, in a > vector x, > I would do something like > > library(hgu95av2) > mysyms = unlist(mget(x, hgu95av2SYMBOL)) > > if what you want is to first, find all genes that have a GO > annotation, given a chip you can use > the mappings in hgu95av2GO2PROBE or hgu95av2GO2ALLPROBES (and I will > leave it to you to read the manual pages and find out what the > difference is) > eg. > > hgu95av2GO2ALLPROBES$"GO:0000022" > TAS > "37171_at" > > and then > > hgu95av2SYMBOL$"37171_at" > [1] "KIF23" > > Robert > > On Feb 24, 2005, at 6:53 AM, Katleen De Preter wrote: > >> Dear colleagues, >> I have a little question about managing data from the GoHyperG >> function. >> I would like to obtain a table with the 20 most significant BP-GO >> terms of a genelist (obtained with SAM), the p-values, the >> discription of the GO term and a column with the gene-names >> (comma-separated) from the genelist that belong to these GO terms. >> How can I obtain this last column??? >> >> I managed to obtain the 3 first columns with: >> GOtest<-GOHyperG(genelist,what="BP") >> table<-data.frame(sort(GOtest$pvalues)[1:t],GOtest$intCounts[1: >> t],goterms[rownames(as.matrix(GOtest$intCounts[1:t]))]) >> >> Thank you in advance! >> Katleen De Preter >> >> >> >> -- >> 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 > | > +------------------------------------------------------------------- ---- > ----------------+ > -- *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.