Dear Bioconductors, I tried to apply the code in "An Introduction to GSEABase" to my ExpressionSet. Everything works fine until I got the following error message: > mapIdentifiers(egs, EntrezIdentifier()) Fehler: getAnnMap: package ra1r3cdf_1.22.0 not available Here is some more information: > eset ExpressionSet (storageMode: lockedEnvironment) assayData: 29214 features, 26 samples element names: exprs phenoData sampleNames: A1_3, A1_4, ..., T3_3 (26 total) varLabels and varMetadata description: Substance: Substance Period: Incubation Period PrPe: Probe.Period featureData featureNames: 10700001, 10700002, ..., 10940690 (29214 total) fvarLabels and fvarMetadata description: none experimentData: use 'experimentData(object)' Annotation: ra1r3cdf_1.22.0 > sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETAR Y= German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ra1r3cdf_1.22.0 GO.db_2.2.11 [3] ragene10sttranscriptcluster.db_1.0.1 RSQLite_0.7-1 [5] DBI_0.2-4 GSEABase_1.6.1 [7] graph_1.22.2 annotate_1.22.0 [9] AnnotationDbi_1.6.1 Biobase_2.4.1 loaded via a namespace (and not attached): [1] tools_2.9.0 XML_2.5-1 xtable_1.5-5 Any help is appreciated Thank you Nikolaus [[alternative HTML version deleted]]

Hi Nikolaus, Nikolaus Schantz wrote: > Dear Bioconductors, > > > > I tried to apply the code in "An Introduction to GSEABase" to my > ExpressionSet. > > > > Everything works fine until I got the following error message: > > > >> mapIdentifiers(egs, EntrezIdentifier()) > > Fehler: getAnnMap: package ra1r3cdf_1.22.0 not available > > > > Here is some more information: > > > >> eset > > ExpressionSet (storageMode: lockedEnvironment) > > assayData: 29214 features, 26 samples > > element names: exprs > > phenoData > > sampleNames: A1_3, A1_4, ..., T3_3 (26 total) > > varLabels and varMetadata description: > > Substance: Substance > > Period: Incubation Period > > PrPe: Probe.Period > > featureData > > featureNames: 10700001, 10700002, ..., 10940690 (29214 total) > > fvarLabels and fvarMetadata description: none > > experimentData: use 'experimentData(object)' > > Annotation: ra1r3cdf_1.22.0 This is undoubtedly the source of your problem. The annotation of your ExpressionSet shouldn't be something like that. The most likely correct annotation is 'ra1r3', assuming this is a custom chip of that name. However, looking at your sessionInfo(), I get the impression that this might actually be a rat gene st chip, and if I further surmise that you want to annotate using the ragene10sttranscriptcluster.db_1.0.1 package you have attached, then the annotation should be 'ragene10sttranscriptcluster'. If I have guessed correctly, then you should be able to proceed after adjusting the annotation slot of your ExpressionSet: annotation(eset) <- "ragene10sttranscriptcluster" Best, Jim > > > >> sessionInfo() > > R version 2.9.0 (2009-04-17) > > i386-pc-mingw32 > > > > locale: > > LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONET ARY= > German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > > other attached packages: > > [1] ra1r3cdf_1.22.0 GO.db_2.2.11 > > > [3] ragene10sttranscriptcluster.db_1.0.1 RSQLite_0.7-1 > > > [5] DBI_0.2-4 GSEABase_1.6.1 > > > [7] graph_1.22.2 annotate_1.22.0 > > > [9] AnnotationDbi_1.6.1 Biobase_2.4.1 > > > > > loaded via a namespace (and not attached): > > [1] tools_2.9.0 XML_2.5-1 xtable_1.5-5 > > > > Any help is appreciated > > Thank you > > Nikolaus > > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826