Hi Alice -- "Johnstone, Alice" <alice.johnstone at="" esr.cri.nz=""> writes: > Hi, > I am having some trouble creating a geneset collection for GO data from > the Illumina annotation package illuminaRatBCv1. I can create the KEGG > set fine as shown below, but when I try the same for GO info I get the > error below: > >> > illumina.rat.kegg<-GeneSetCollection(idType=AnnotationIdentifier("il lumi > naRatBCv1"),setType=KEGGCollection()) >> illumina.rat.kegg > GeneSetCollection > names: 04110, 00400, ..., 00640 (184 total) > unique identifiers: 2260270, 5900358, ..., 580441 (2557 total) > types in collection: > geneIdType: AnnotationIdentifier (1 total) > collectionType: KEGGCollection (1 total) > > >> > illumina.rat.go<-GeneSetCollection(idType=AnnotationIdentifier("illu mina > RatBCv1"),setType=GOCollection()) > Error in as.vector(x, "character") : > cannot coerce type 'S4' to vector of type 'character' > Error in as.list(getAnnMap("GO2PROBE", idType)) : > error in evaluating the argument 'x' in selecting a method for > function 'as.list' Bug, unfortunately, should be fixed in GSEABase_1.2.2 available noon tomorrow PST. Sorry about that, Martin > Could someone help me out with whats going wrong? > Thank you! > Alice > > > >> sessionInfo() > R version 2.7.0 (2008-04-22) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New > Zealand.1252;LC_MONETARY=English_New > Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252 > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > > [8] base > > other attached packages: > [1] GO.db_2.2.0 GSEABase_1.2.1 illuminaRatBCv1_1.1.0 > [4] beadarray_1.8.0 affy_1.18.0 preprocessCore_1.2.0 > [7] affyio_1.8.0 geneplotter_1.18.0 annotate_1.18.0 > [10] xtable_1.5-2 AnnotationDbi_1.2.0 RSQLite_0.6-8 > [13] DBI_0.2-4 lattice_0.17-6 Biobase_2.0.1 > [16] limma_2.14.1 > > loaded via a namespace (and not attached): > [1] cluster_1.11.10 graph_1.18.0 grid_2.7.0 > KernSmooth_2.22-22 > [5] RColorBrewer_1.0-2 XML_1.93-2.1 > > > > > Alice Johnstone > > PhD Student > Institute of Environmental Science and Research Ltd > Kenepuru Science Centre > 34 Kenepuru Drive > PO Box 50-348 > Porirua > New Zealand > > Tel: + 64 4 914-0717 > Fax: + 64 4 914-0770 > > > P Think before you print > This e-mail transmission and any attachments that accompany it may contain information that is privileged, confidential or otherwise exempt from disclosure under applicable law and is intended solely for the use of the individual(s) to whom it was intended to be addressed. > If you have received this e-mail by mistake, or you are not the intended recipient, any disclosure, dissemination, distribution, copying or other use or retention of this communication or its substance is prohibited. If you have received this communication in error, please immediately reply to the author via e-mail that you received this message by mistake and also permanently delete the original and all copies of this e-mail and any attachments from your computer. Thank you. > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793