This is the code I used: gse <- getGEO(filename='GSE19380_family.soft') with the "GSE19380_family.soft" downloaded on my computer. Then GDS2eSet(gse, do.log2=FALSE,GPL=NULL,AnnotGPL=TRUE) And I receive this error: Error in getGEO(Meta(GDS)$platform, AnnotGPL = AnnotGPL) : You must supply either a filename of a GEO file or a GEO accession Any help would be appreciated Thanks in advance -- output of sessionInfo(): > sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] GEOquery_2.24.1 CellMix_1.1 GSEABase_1.20.1 graph_1.36.1 [5] annotate_1.36.0 AnnotationDbi_1.20.3 stringr_0.6.2 Rcpp_0.10.2 [9] NMF_0.10.1 Biobase_2.18.0 BiocGenerics_0.4.0 bigmemory_4.3.0 [13] bigmemory.sri_0.1.2 digest_0.6.2 registry_0.2 rngtools_1.1 [17] pkgmaker_0.10.1 loaded via a namespace (and not attached): [1] beeswarm_0.1.5 codetools_0.2-8 colorspace_1.2-1 [4] corpcor_1.6.4 csSAM_1.2.1 DBI_0.2-5 [7] doParallel_1.0.1 foreach_1.4.0 genefilter_1.40.0 [10] gridBase_0.4-6 gtools_2.7.0 IRanges_1.16.4 [13] iterators_1.0.6 limSolve_1.5.3 matrixStats_0.6.2 [16] parallel_2.15.2 preprocessCore_1.20.0 quadprog_1.5-4 [19] R.methodsS3_1.4.2 RColorBrewer_1.0-5 RCurl_1.95-3 [22] RSQLite_0.11.2 splines_2.15.2 stats4_2.15.2 [25] survival_2.37-2 tools_2.15.2 XML_3.95-0.1 [28] xtable_1.7-0 -- Sent via the guest posting facility at bioconductor.org.

Hi Laurent, On 2/7/2013 11:52 AM, Laurent Pays [guest] wrote: > This is the code I used: > gse<- getGEO(filename='GSE19380_family.soft') with the "GSE19380_family.soft" downloaded on my computer. > > Then > GDS2eSet(gse, do.log2=FALSE,GPL=NULL,AnnotGPL=TRUE) I think the problem is that you are getting a GSE object, not a GDS object. The easiest thing to do is just get the GSE object and go from there: > gse <- getGEO("GSE19380") <snip> > gse[[1]] ExpressionSet (storageMode: lockedEnvironment) assayData: 31099 features, 26 samples element names: exprs protocolData: none phenoData sampleNames: GSM480943 GSM480944 ... GSM480968 (26 total) varLabels: title geo_accession ... data_row_count (33 total) varMetadata: labelDescription featureData featureNames: 1367452_at 1367453_at ... AFFX_ratb2/X14115_at (31099 total) fvarLabels: ID GB_ACC ... Gene Ontology Molecular Function (16 total) fvarMetadata: Column Description labelDescription experimentData: use 'experimentData(object)' Annotation: GPL1355 So you don't have to convert to an ExpressionSet, as you already have one. Best, Jim > > And I receive this error: > > Error in getGEO(Meta(GDS)$platform, AnnotGPL = AnnotGPL) : > You must supply either a filename of a GEO file or a GEO accession > > Any help would be appreciated > > Thanks in advance > > -- output of sessionInfo(): > >> sessionInfo() > R version 2.15.2 (2012-10-26) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8 > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods base > > other attached packages: > [1] GEOquery_2.24.1 CellMix_1.1 GSEABase_1.20.1 graph_1.36.1 > [5] annotate_1.36.0 AnnotationDbi_1.20.3 stringr_0.6.2 Rcpp_0.10.2 > [9] NMF_0.10.1 Biobase_2.18.0 BiocGenerics_0.4.0 bigmemory_4.3.0 > [13] bigmemory.sri_0.1.2 digest_0.6.2 registry_0.2 rngtools_1.1 > [17] pkgmaker_0.10.1 > > loaded via a namespace (and not attached): > [1] beeswarm_0.1.5 codetools_0.2-8 colorspace_1.2-1 > [4] corpcor_1.6.4 csSAM_1.2.1 DBI_0.2-5 > [7] doParallel_1.0.1 foreach_1.4.0 genefilter_1.40.0 > [10] gridBase_0.4-6 gtools_2.7.0 IRanges_1.16.4 > [13] iterators_1.0.6 limSolve_1.5.3 matrixStats_0.6.2 > [16] parallel_2.15.2 preprocessCore_1.20.0 quadprog_1.5-4 > [19] R.methodsS3_1.4.2 RColorBrewer_1.0-5 RCurl_1.95-3 > [22] RSQLite_0.11.2 splines_2.15.2 stats4_2.15.2 > [25] survival_2.37-2 tools_2.15.2 XML_3.95-0.1 > [28] 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099