Hello, I am trying to do GO enrichment analysis. When I use ???GOFrame???, I get the following error message: > frame = toTable(org.Rn.egGO) > goframeData = data.frame(frame$go_id, frame$Evidence, frame$gene_id) > goFrame = GOFrame(goframeData, organism = "Rattus norvegicus") Error in .testGOFrame(x, organism) : All of the Evidence codes in your data.frame object must be legitimate Evidence Codes. I checked the BioC mail list and noticed that same error was discussed before at: https://stat.ethz.ch/pipermail/bioconductor/2012-May/045773.html It was mentioned that a bug was fixed in AnnotationDbi version 1.18.1. I am using the most recent version AnnotationDbi version 1.18.4. Could this be the source of error? Any help is greatly appreciated. Thanks, Diwan -- output of sessionInfo(): > sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rat2302cdf_2.10.0 KEGG.db_2.7.1 BiocInstaller_1.4.9 GSEABase_1.18.0 rat2302.db_2.7.1 [6] org.Rn.eg.db_2.7.1 annotate_1.34.1 GOstats_2.22.0 graph_1.34.0 Category_2.22.0 [11] GO.db_2.7.1 RSQLite_0.11.1 DBI_0.2-5 AnnotationDbi_1.18.4 Biobase_2.16.0 loaded via a namespace (and not attached): [1] genefilter_1.38.0 IRanges_1.12.6 RBGL_1.30.1 splines_2.15.2 survival_2.37-4 tools_2.15.2 [7] XML_3.9-4 xtable_1.7-0 -- Sent via the guest posting facility at bioconductor.org.

Hi Diwan, 1.18.4 is not the most current release version. You can see the build reports and most current versions here, http://bioconductor.org/checkResults/release/bioc-LATEST/ http://bioconductor.org/checkResults/devel/bioc-LATEST/ The code below is working for me with both AnnotationDbi 1.20.7 (release) and 1.21.16 (devel). > frame = toTable(org.Rn.egGO) > goframeData = data.frame(frame$go_id, frame$Evidence, frame$gene_id) > goFrame = GOFrame(goframeData, organism = "Rattus norvegicus") Loading required package: GO.db > sessionInfo() R version 2.15.2 RC (2012-10-24 r61009) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GO.db_2.8.0 GOstats_2.24.0 graph_1.36.2 [4] Category_2.24.0 org.Rn.eg.db_2.8.1 RSQLite_0.11.2 [7] DBI_0.2-5 AnnotationDbi_1.20.7 Biobase_2.18.0 [10] BiocGenerics_0.4.0 BiocInstaller_1.8.3 loaded via a namespace (and not attached): [1] annotate_1.36.0 AnnotationForge_1.0.3 genefilter_1.40.0 [4] GSEABase_1.20.2 IRanges_1.16.6 parallel_2.15.2 [7] RBGL_1.34.0 splines_2.15.2 stats4_2.15.2 [10] survival_2.37-4 tools_2.15.2 XML_3.95-0.1 Valerie On 03/19/13 09:02, Diwan [guest] wrote: > > Hello, > I am trying to do GO enrichment analysis. When I use ???GOFrame???, I get the following error message: >> frame = toTable(org.Rn.egGO) >> goframeData = data.frame(frame$go_id, frame$Evidence, frame$gene_id) >> goFrame = GOFrame(goframeData, organism = "Rattus norvegicus") > Error in .testGOFrame(x, organism) : > All of the Evidence codes in your data.frame object must be legitimate Evidence Codes. > > I checked the BioC mail list and noticed that same error was discussed before at: > https://stat.ethz.ch/pipermail/bioconductor/2012-May/045773.html > It was mentioned that a bug was fixed in AnnotationDbi version 1.18.1. I am using the most recent version AnnotationDbi version 1.18.4. > Could this be the source of error? Any help is greatly appreciated. > Thanks, > Diwan > > > -- output of sessionInfo(): > >> sessionInfo() > R version 2.15.2 (2012-10-26) > Platform: x86_64-redhat-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] rat2302cdf_2.10.0 KEGG.db_2.7.1 BiocInstaller_1.4.9 GSEABase_1.18.0 rat2302.db_2.7.1 > [6] org.Rn.eg.db_2.7.1 annotate_1.34.1 GOstats_2.22.0 graph_1.34.0 Category_2.22.0 > [11] GO.db_2.7.1 RSQLite_0.11.1 DBI_0.2-5 AnnotationDbi_1.18.4 Biobase_2.16.0 > > loaded via a namespace (and not attached): > [1] genefilter_1.38.0 IRanges_1.12.6 RBGL_1.30.1 splines_2.15.2 survival_2.37-4 tools_2.15.2 > [7] XML_3.9-4 xtable_1.7-0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >