Many thanks for your prompt reply Vincent! Initially, it looked trivial and it did work, but!... How can my ExpressionSet from 34760 features go down to 85? It can't be possible that in that chip there are only 85 probe sets with Entrez ID, or? Dave Date: Mon, 31 May 2010 02:28:40 -0400 Subject: Re: [BioC] mogene10stv1 annotation problem From: stvjc@channing.harvard.edu To: arhaios50@hotmail.com CC: bioconductor@stat.math.ethz.ch because you have set require.entrez=TRUE, some mapping package must be used to check for entrez ids that correspond to the featureName elements of your ExpressionSet. annotation(vsnrmadata) evaluates to "mogene10stv1", and AFAIK there is no bioconductor annotation package with that name (although you could make one if you wanted to). Because your sessionInfo suggests that mogene10stprobeset.db_5.0.1 is a mapping that you are interested in, you could probably do annotation(vsnrmadata) = "mogene10stprobeset.db" and get better results with your nsFilter call. On Sun, May 30, 2010 at 1:59 PM, Dave Crawford <arhaios50@hotmail.com> wrote: Dear list, I am trying the following and I am getting an error. Could you help me please? Thanks! Dave > vsnrmadata ExpressionSet (storageMode: lockedEnvironment) assayData: 34760 features, 12 samples element names: exprs protocolData sampleNames: 01_V12_1.CEL, 02_V12_2.CEL, ..., 12_D12_3.CEL (12 total) varLabels and varMetadata description: ScanDate: NA phenoData sampleNames: 01_V12_1.CEL, 02_V12_2.CEL, ..., 12_D12_3.CEL (12 total) varLabels and varMetadata description: Treatment: featureData: none experimentData: use 'experimentData(object)' Annotation: mogene10stv1 > fvsnrmadata = nsFilter(vsnrmadata, require.entrez = TRUE, require.GOBP = FALSE, require.GOCC = FALSE, require.GOMF = FALSE, var.filter = FALSE)$eset Error: getAnnMap: package mogene10stv1 not available > sessionInfo() R version 2.11.0 (2010-04-22) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] limma_3.4.0 mogene10stprobeset.db_5.0.1 org.Mm.eg.db_2.4.1 RSQLite_0.8-4 DBI_0.2-5 AnnotationDbi_1.10.0 [7] genefilter_1.30.0 vsn_3.16.0 mogene10stv1cdf_2.6.0 affy_1.26.0 Biobase_2.8.0 loaded via a namespace (and not attached): [1] affyio_1.16.0 annotate_1.26.0 grid_2.11.0 lattice_0.18-5 preprocessCore_1.10.0 splines_2.11.0 survival_2.35-8 tools_2.11.0 [9] xtable_1.5-6 _________________________________________________________________ We want to hear all your funny, exciting and crazy Hotmail stories. Tell us now [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor _________________________________________________________________ Do you have a story that started on Hotmail? Tell us now [[alternative HTML version deleted]]