Hi, I am not doing any microarray experiments. However, i still have a set of genes. Of these according to different criteria a sub-set of genes 'becomes' the interesting set of genes. The criteria are for me to decide. Is it possible to to a GO term enrichment on such data. I have NCBI GeneIDs for all the genes under study. regards --sameet

Yes, GOstats and topGO will do these things for you. Both have pretty good vignettes and GOstats usage is described in some detail in http://www.bioconductor.org/pub/biocases/ Sameet Mehta wrote: > Hi, > I am not doing any microarray experiments. However, i still have a set > of genes. Of these according to different criteria a sub-set of genes > 'becomes' the interesting set of genes. The criteria are for me to > decide. Is it possible to to a GO term enrichment on such data. > I have NCBI GeneIDs for all the genes under study. > > regards > --sameet > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- 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

If you must do this in Bioc, use something like topGO, but it would be much easier to use fatigo www.fatigo.org) -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Sameet Mehta Sent: 18 September 2008 15:28 To: bioconductor at stat.math.ethz.ch Subject: [BioC] Query about GO term enrichment Hi, I am not doing any microarray experiments. However, i still have a set of genes. Of these according to different criteria a sub-set of genes 'becomes' the interesting set of genes. The criteria are for me to decide. Is it possible to to a GO term enrichment on such data. I have NCBI GeneIDs for all the genes under study. regards --sameet _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor