How to get affyId from GOstats output
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alex lam RI ▴ 310
@alex-lam-ri-1491
Last seen 7.7 years ago
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
GO rae230a GO rae230a • 653 views
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@james-w-macdonald-5106
Last seen 16 hours ago
United States
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
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