Dear list, I found "annotate::getAnnMap" seems not working for R-2.14.0. What I have is KEGG pathway ids, and I would like to return the pathway names using the following scenario commands: > library(Category) > keggID<-"04940" > getPathNames(keggID) Error: getAnnMap: package KEGG not available Also, the same Error message showed up when I try to use the 'summary()' function after "GOstats::hyperGTest". I would appreciate very much if it can be confirmed that this is a R/Bioconductor problem rather than a local one. Thank you very much in advance! > sessionInfo() R version 2.14.0 Patched (2011-11-25 r57751) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_IE.UTF-8/en_IE.UTF-8/en_IE.UTF-8/C/en_IE.UTF-8/en_IE.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] annotate_1.32.0 org.Hs.eg.db_2.6.4 limma_3.10.0 [4] affy_1.32.0 BiocInstaller_1.2.1 GOstats_2.20.0 [7] RSQLite_0.11.1 DBI_0.2-5 graph_1.32.0 [10] Category_2.20.0 AnnotationDbi_1.16.10 Biobase_2.14.0 loaded via a namespace (and not attached): [1] affyio_1.22.0 genefilter_1.36.0 GO.db_2.6.1 [4] GSEABase_1.16.0 IRanges_1.12.5 preprocessCore_1.16.0 [7] RBGL_1.30.1 splines_2.14.0 survival_2.36-10 [10] tools_2.14.0 XML_3.6-2 xtable_1.6-0 [13] zlibbioc_1.0.0 Cheers, Yuan

On Fri, Dec 16, 2011 at 7:11 AM, Yuan Hao <yuan.x.hao@gmail.com> wrote: > Dear list, > > I found "annotate::getAnnMap" seems not working for R-2.14.0. > > What I have is KEGG pathway ids, and I would like to return the pathway > names using the following scenario commands: > > > library(Category) > > keggID<-"04940" > > getPathNames(keggID) > Error: getAnnMap: package KEGG not available > > Hi, Yuan. This is not a bug, but the error message makes it sound worse than it really is. You'll just need to install the KEGG.db package. http://bioconductor.org/packages/release/data/annotation/html/KEGG.db. html Sean > Also, the same Error message showed up when I try to use the 'summary()' > function after "GOstats::hyperGTest". I would appreciate very much if it > can be confirmed that this is a R/Bioconductor problem rather than a local > one. Thank you very much in advance! > > > > sessionInfo() > R version 2.14.0 Patched (2011-11-25 r57751) > Platform: x86_64-apple-darwin9.8.0/x86_**64 (64-bit) > > locale: > [1] en_IE.UTF-8/en_IE.UTF-8/en_IE.**UTF-8/C/en_IE.UTF-8/en_IE.UTF-**8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] annotate_1.32.0 org.Hs.eg.db_2.6.4 limma_3.10.0 > [4] affy_1.32.0 BiocInstaller_1.2.1 GOstats_2.20.0 > [7] RSQLite_0.11.1 DBI_0.2-5 graph_1.32.0 > [10] Category_2.20.0 AnnotationDbi_1.16.10 Biobase_2.14.0 > > loaded via a namespace (and not attached): > [1] affyio_1.22.0 genefilter_1.36.0 GO.db_2.6.1 > [4] GSEABase_1.16.0 IRanges_1.12.5 preprocessCore_1.16.0 > [7] RBGL_1.30.1 splines_2.14.0 survival_2.36-10 > [10] tools_2.14.0 XML_3.6-2 xtable_1.6-0 > [13] zlibbioc_1.0.0 > > Cheers, > Yuan > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > [[alternative HTML version deleted]]