Dear colleagues, After running hyperGTest, summary(hgOver) returns a table of GO IDs, Pvalues, Count ...etc For example, for a particular GO term the Count = 3 and Size = 9. How do I retrieve the affyIDs of those 3 and 9 genes? Many thanks, Alex > sessionInfo() R version 2.6.1 (2007-11-26) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] GOstats_2.4.0 Category_2.4.0 genefilter_1.16.0 [4] survival_2.34 RBGL_1.14.0 graph_1.16.1 [7] annotate_1.16.1 xtable_1.5-2 GO.db_2.0.2 [10] rae230a.db_2.0.2 AnnotationDbi_1.0.6 RSQLite_0.6-7 [13] DBI_0.2-4 Biobase_1.16.2 loaded via a namespace (and not attached): [1] cluster_1.11.9 rcompgen_0.1-17 > -------------------------------------------- Alex C. Lam Roslin Institute (Edinburgh) Midlothian EH25 9PS United Kingdom Tel: +44 131 5274471 Roslin Institute is a company limited by guarantee, registered in Scotland (registered number SC157100) and a Scottish Charity (registered number SC023592). Our registered office is at Roslin, Midlothian, EH25 9PS. VAT registration number 847380013. The information contained in this e-mail (including any attachments) is confidential and is intended for the use of the addressee only. The opinions expressed within this e-mail (including any attachments) are the opinions of the sender and do not necessarily constitute those of Roslin Institute (Edinburgh) ("the Institute") unless specifically stated by a sender who is duly authorised to do so on behalf of the Institute

Hi Alex, See ?probeSetSummary. You might be interested in hyperGoutput() in the affycoretools package. Best, Jim alex lam (RI) wrote: > Dear colleagues, > > After running hyperGTest, summary(hgOver) returns a table of GO IDs, > Pvalues, Count ...etc > > For example, for a particular GO term the Count = 3 and Size = 9. How do > I retrieve the affyIDs of those 3 and 9 genes? > > Many thanks, > Alex > >> sessionInfo() > R version 2.6.1 (2007-11-26) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > Kingdom.1252;LC_MONETARY=English_United > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > > [8] methods base > > other attached packages: > [1] GOstats_2.4.0 Category_2.4.0 genefilter_1.16.0 > [4] survival_2.34 RBGL_1.14.0 graph_1.16.1 > [7] annotate_1.16.1 xtable_1.5-2 GO.db_2.0.2 > [10] rae230a.db_2.0.2 AnnotationDbi_1.0.6 RSQLite_0.6-7 > [13] DBI_0.2-4 Biobase_1.16.2 > > loaded via a namespace (and not attached): > [1] cluster_1.11.9 rcompgen_0.1-17 > > -------------------------------------------- > Alex C. Lam > Roslin Institute (Edinburgh) > Midlothian > EH25 9PS > United Kingdom > Tel: +44 131 5274471 > > Roslin Institute is a company limited by guarantee, registered in > Scotland (registered number SC157100) and a Scottish Charity (registered > number SC023592). Our registered office is at Roslin, Midlothian, EH25 > 9PS. VAT registration number 847380013. > > The information contained in this e-mail (including any attachments) is > confidential and is intended for the use of the addressee only. The > opinions expressed within this e-mail (including any attachments) are > the opinions of the sender and do not necessarily constitute those of > Roslin Institute (Edinburgh) ("the Institute") unless specifically > stated by a sender who is duly authorised to do so on behalf of the > Institute > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623