Hi Seth, I had a problem earlier with an invalid GO term that was throwing up an error. You advised to update all my packages, which I thought solved the problem. However, the problem reappeared later when I reran my script, and I've figured out the difference is what other packages I have loaded. I have a complete R session below, where I first only load GOstats, then call hyperGTest on a GOHyperGParams object, which tests 1139 GO BP ids, and 44 have p < 0.001. Next I load affycoretools, then call hyperGTest on the exact same object, which now tests 1146 GO BP ids, and 46 have p < 0.001. Loading affycoretools in turn loads package GO, which then masks many functions from package GO.db - maybe this is where the problem is? I'm fine because I can get the problematic GO term to disappear, but it seems like the discordance between the packages is a bug. Thanks, Jenny R version 2.6.0 Under development (unstable) (2007-08-28 r42679) Copyright (C) 2007 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > setwd("C:/statistics/anshuman") > load("anshuman2.RData") > library(GOstats) Loading required package: graph Loading required package: GO.db Loading required package: AnnotationDbi Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: DBI Loading required package: RSQLite Loading required package: annotate Loading required package: RBGL Loading required package: Category Loading required package: genefilter Loading required package: survival Loading required package: splines > library(ath1121501) Attaching package: 'ath1121501' The following object(s) are masked _by_ .GlobalEnv : ath1121501ENTREZID > SVC.up.BP.results.cond <- hyperGTest(SVC.up.BP.cond) > SVC.up.BP.results.cond Gene to GO BP Conditional test for over-representation 1139 GO BP ids tested (44 have p < 0.001) Selected gene set size: 1603 Gene universe size: 12763 Annotation package: ath1121501 > sessionInfo() R version 2.6.0 Under development (unstable) (2007-08-28 r42679) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] ath1121501_1.17.0 GOstats_2.3.16 Category_2.3.36 [4] genefilter_1.15.11 survival_2.32 RBGL_1.13.6 [7] annotate_1.15.7 GO.db_1.17.1 AnnotationDbi_0.1.14 [10] RSQLite_0.6-2 DBI_0.2-3 Biobase_1.15.33 [13] graph_1.15.16 loaded via a namespace (and not attached): [1] cluster_1.11.7 simpleaffy_2.13.01 > library(affycoretools) Loading required package: affy Loading required package: affyio Loading required package: preprocessCore Loading required package: limma Loading required package: biomaRt Loading required package: XML Attaching package: 'XML' The following object(s) are masked from package:graph : addNode Loading required package: RCurl Attaching package: 'biomaRt' The following object(s) are masked from package:annotate : getGO Loading required package: gcrma Loading required package: matchprobes Loading required package: xtable Loading required package: annaffy Loading required package: GO Attaching package: 'GO' The following object(s) are masked from package:GO.db : GOBPANCESTOR, GOBPCHILDREN, GOBPOFFSPRING, GOBPPARENTS, GOCCANCESTOR, GOCCCHILDREN, GOCCOFFSPRING, GOCCPARENTS, GOMAPCOUNTS, GOMFANCESTOR, GOMFCHILDREN, GOMFOFFSPRING, GOMFPARENTS, GOOBSOLETE, GOSYNONYM, GOTERM Loading required package: KEGG > SVC.up.BP.results.cond <- hyperGTest(SVC.up.BP.cond) > SVC.up.BP.results.cond Gene to GO BP Conditional test for over-representation 1146 GO BP ids tested (46 have p < 0.001) Selected gene set size: 1603 Gene universe size: 12766 Annotation package: ath1121501 > sessionInfo() R version 2.6.0 Under development (unstable) (2007-08-28 r42679) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] affycoretools_1.9.4 annaffy_1.9.4 KEGG_1.17.0 [4] GO_1.17.0 xtable_1.5-1 gcrma_2.9.1 [7] matchprobes_1.9.10 biomaRt_1.11.9 RCurl_0.8-1 [10] XML_1.9-0 limma_2.11.12 affy_1.15.8 [13] preprocessCore_0.99.13 affyio_1.5.10 ath1121501_1.17.0 [16] GOstats_2.3.16 Category_2.3.36 genefilter_1.15.11 [19] survival_2.32 RBGL_1.13.6 annotate_1.15.7 [22] GO.db_1.17.1 AnnotationDbi_0.1.14 RSQLite_0.6-2 [25] DBI_0.2-3 Biobase_1.15.33 graph_1.15.16 loaded via a namespace (and not attached): [1] cluster_1.11.7 simpleaffy_2.13.01 > At 01:41 PM 9/11/2007, Jenny Drnevich wrote: >Hi Seth, > >Once again, updating packages solved the problem! They must have >been VERY recent updates - I only installed R-devel last week! I >guess that's the nature of R, especially right before a new release. > >Many thanks, >Jenny > >At 11:57 AM 9/11/2007, Seth Falcon wrote: > >Hi Jenny, > > > >Jenny Drnevich <drnevich at="" uiuc.edu=""> writes: > > > I posted this message last week, but didn't get any responses. I've > > > been trying everything I can think of to remove this one problematic > > > GO term from my HyperGResult object so I can get the other 45 > > > overrepresented GO terms, but I'm not having any luck. I would > > > appreciate any suggestions!!! > > > >Sorry, things have been a bit busy around here :-) > > > > > At 12:22 PM 9/5/2007, Jenny Drnevich wrote: > > >>Hi everyone, > > >> > > >>I'm doing hypergeometric testing of GO terms using GOstats on some > > >>data from ath1121501 Affy arrays. I had some trouble figuring out how > > >>to work with these arrays at first because the annotation package > > >>doesn't include EntrezIDs, but after searching the archives I found > > >>all you had to do was this to get it to work: > > >> > > >>ath1121501ENTREZID <- ath1121501ACCNUM > > >> > > >>Anyway, everything was going fine, expect in one my HyperGResult > > >>objects there is a significant GO term that throws up an error: > > >> > > >> >SVC.up.BP <- new("GOHyperGParams", geneIds = > > >>entrezUniverse.sortVctrl[EID.sortVctrl==1], > > >> universeGeneIds = entrezUniverse.sortVctrl, > > >>annotation = "ath1121501", > > >> ontology = "BP", pvalueCutoff = hgCutoff, > > >> conditional = FALSE, > > >> testDirection = "over") > > >> > > >> >SVC.up.BP.results <- hyperGTest(SVC.up.BP) > > >> > > >> >summary(SVC.up.BP.results) > > >>Error in .checkKeys(value, Lkeys(x), x at ifnotfound) : > > >> invalid key "GO:0002226" > > > >First, can you try updating your packages. We've very recently pushed > >out new candidates for annotation as well as some bug fixes for > >AnnotationDbi. > > > >If the problem persists, can you send me (off-list) an rda file > >containing your SVC.up.BP object? > > > >+ seth > > > >-- > >Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center > >BioC: http://bioconductor.org/ > >Blog: http://userprimary.net/user/ > >_______________________________________________ >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