dear list, I cannot get to work GOstats with the annotation for E. coli in org.EcK12.eg.db. Please find below the code that reproduces the problem including the error message, and my sessionInfo() at the end of this email. I have included the same exercise with the human annotation package org.Hs.eg.db which runs fine in my system. Any help with this will be very much appreciated. thanks!! robert. ==========CODE STARTS HERE=========== library(org.Hs.eg.db) library(org.EcK12.eg.db) library(GOstats) geneuniverse <- mappedkeys(org.EcK12.egSYMBOL) set.seed(12345) geneset <- sample(geneuniverse, size=100, replace=FALSE) goHypGparams <- new("GOHyperGParams", geneIds=geneset, universeGeneIds=geneuniverse, annotation="org.EcK12.eg.db", ontology="BP", pvalueCutoff=1.0, conditional=TRUE, testDirection="over") goHypGcond <- hyperGTest(goHypGparams) Error in get(mapName, envir = pkgEnv, inherits = FALSE) : variable "org.EcK12.egENTREZID" was not found Error in mget(probes, ID2EntrezID(datPkg)) : error in evaluating the argument 'envir' in selecting a method for function 'mget' geneuniverse <- mappedkeys(org.Hs.egSYMBOL) set.seed(12345) geneset <- sample(geneuniverse, size=100, replace=FALSE) goHypGparams <- new("GOHyperGParams", geneIds=geneset, universeGeneIds=geneuniverse, annotation="org.Hs.eg.db", ontology="BP", pvalueCutoff=1.0, conditional=TRUE, testDirection="over") goHypGcond <- hyperGTest(goHypGparams) sessionInfo() R version 2.8.0 beta (2008-10-05 r46601) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] org.Hs.eg.db_2.2.6 GOstats_2.7.0 Category_2.7.6 [4] genefilter_1.21.5 survival_2.34-1 RBGL_1.17.2 [7] annotate_1.19.2 xtable_1.5-4 GO.db_2.2.5 [10] graph_1.19.6 org.EcK12.eg.db_2.2.6 AnnotationDbi_1.3.12 [13] RSQLite_0.7-0 DBI_0.2-4 Biobase_2.1.7 loaded via a namespace (and not attached): [1] cluster_1.11.11 GSEABase_1.3.6 XML_1.98-1

Hi Robert, Yet another one that I will need to write some specialized code for. I should get it done by the end of the week, and will push it to both release and devel. I will post an email when it is done, best wishes Robert Robert Castelo wrote: > dear list, > > I cannot get to work GOstats with the annotation for E. coli in > org.EcK12.eg.db. Please find below the code that reproduces the problem > including the error message, and my sessionInfo() at the end of this > email. I have included the same exercise with the human annotation > package org.Hs.eg.db which runs fine in my system. Any help with this > will be very much appreciated. > > thanks!! > robert. > ==========CODE STARTS HERE=========== > > library(org.Hs.eg.db) > library(org.EcK12.eg.db) > library(GOstats) > > geneuniverse <- mappedkeys(org.EcK12.egSYMBOL) > set.seed(12345) > geneset <- sample(geneuniverse, size=100, replace=FALSE) > > > goHypGparams <- new("GOHyperGParams", > geneIds=geneset, > universeGeneIds=geneuniverse, > annotation="org.EcK12.eg.db", ontology="BP", > pvalueCutoff=1.0, conditional=TRUE, > testDirection="over") > > goHypGcond <- hyperGTest(goHypGparams) > > Error in get(mapName, envir = pkgEnv, inherits = FALSE) : > variable "org.EcK12.egENTREZID" was not found > Error in mget(probes, ID2EntrezID(datPkg)) : > error in evaluating the argument 'envir' in selecting a method for > function 'mget' > > geneuniverse <- mappedkeys(org.Hs.egSYMBOL) > set.seed(12345) > geneset <- sample(geneuniverse, size=100, replace=FALSE) > > > goHypGparams <- new("GOHyperGParams", > geneIds=geneset, > universeGeneIds=geneuniverse, > annotation="org.Hs.eg.db", ontology="BP", > pvalueCutoff=1.0, conditional=TRUE, > testDirection="over") > > goHypGcond <- hyperGTest(goHypGparams) > > > sessionInfo() > R version 2.8.0 beta (2008-10-05 r46601) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDEN TIFICATION=C > > attached base packages: > [1] splines tools stats graphics grDevices utils > datasets > [8] methods base > > other attached packages: > [1] org.Hs.eg.db_2.2.6 GOstats_2.7.0 Category_2.7.6 > [4] genefilter_1.21.5 survival_2.34-1 RBGL_1.17.2 > [7] annotate_1.19.2 xtable_1.5-4 GO.db_2.2.5 > [10] graph_1.19.6 org.EcK12.eg.db_2.2.6 AnnotationDbi_1.3.12 > [13] RSQLite_0.7-0 DBI_0.2-4 Biobase_2.1.7 > > loaded via a namespace (and not attached): > [1] cluster_1.11.11 GSEABase_1.3.6 XML_1.98-1 > > _______________________________________________ > 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