I have some basic problems with the ExpressionSet class of Bioconductor (as beginning user). For example, I do the following. gse40012 <- getGEO("GSE40012") es40012 <- gse40012[[1]] a40012<-addGeneInfo(es40012, annotationLibrary = "illuminaHumanv3") Now I want to export the now available annotation from the featureData (e.g `SYMBOL`) together with the expression matrix for post- processing in a different program. How am I doing this? Thanks Chris > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] a4Preproc_1.6.0 illuminaHumanv3.db_1.16.0 hgu133a.db_2.8.0 org.Hs.eg.db_2.8.0 RSQLite_0.11.2 [6] DBI_0.2-5 AnnotationDbi_1.20.3 limma_3.14.3 affy_1.36.0 GEOquery_2.24.0 [11] Biobase_2.18.0 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affyio_1.26.0 AnnotationForge_1.0.3 BiocInstaller_1.8.3 IRanges_1.16.4 parallel_2.15.1 [6] preprocessCore_1.20.0 RCurl_1.95-3 stats4_2.15.1 tools_2.15.1 XML_3.95-0.1 [11] zlibbioc_1.4.0 [[alternative HTML version deleted]]

On Mon, Jan 14, 2013 at 11:00 AM, Forst, Christian <christian.forst at="" mssm.edu=""> wrote: > I have some basic problems with the ExpressionSet class of Bioconductor (as beginning user). > For example, I do the following. > gse40012 <- getGEO("GSE40012") > es40012 <- gse40012[[1]] > a40012<-addGeneInfo(es40012, annotationLibrary = "illuminaHumanv3") > > Now I want to export the now available annotation from the featureData (e.g `SYMBOL`) together with the expression matrix for post-processing in a different program. How am I doing this? > Hi, Christian. Something like this will do the trick. write.table(cbind(fData(a40012)$SYMBOL,exprs(a40012)), file='mydata.txt',sep="\t",row.names=FALSE) Sean > Thanks > Chris > > > > >> sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] a4Preproc_1.6.0 illuminaHumanv3.db_1.16.0 hgu133a.db_2.8.0 org.Hs.eg.db_2.8.0 RSQLite_0.11.2 > [6] DBI_0.2-5 AnnotationDbi_1.20.3 limma_3.14.3 affy_1.36.0 GEOquery_2.24.0 > [11] Biobase_2.18.0 BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] affyio_1.26.0 AnnotationForge_1.0.3 BiocInstaller_1.8.3 IRanges_1.16.4 parallel_2.15.1 > [6] preprocessCore_1.20.0 RCurl_1.95-3 stats4_2.15.1 tools_2.15.1 XML_3.95-0.1 > [11] zlibbioc_1.4.0 > > [[alternative HTML version deleted]] > > _______________________________________________ > 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