Hi all, I am trying to make an AnnotatedDataFrame with the Biobase package. Here is my code: exprsFile<-"D:/exprsData.txt" exprs<-read.table(exprsFile,header=TRUE,sep="",as.is=TRUE) pDataFile<-"D:/pData.txt" pData<-read.table(pDataFile,header=TRUE, sep="", as.is=TRUE) metaData<-"D:/mData.txt" mData<-read.table(metaData,header=TRUE,sep="",as.is=TRUE) metData<-new("AnnotatedDataFrame",data=exprs2,varMetadata=mData) At this step I have the following error: Error in `row.names<-.data.frame`(`*tmp*`, value = c("A", "B")) : length of 'row.names' incorrect It seems strangle because "A" and "B" are the colnames of exprsData (or the rownames of pData). I tried to do : metData<-new("AnnotatedDataFrame",data=exprs2,varMetadata=mData, row.names=1) or rown=rownames(exprs) metData<-new("AnnotatedDataFrame",data=exprs2,varMetadata=mData, row.names=rown) but I steel got the same error hope anyone could help me... > sessionInfo() R version 2.5.0 (2007-04-23) i386-pc-mingw32 locale: LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY= French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252 attached base packages: [1] "tcltk" "splines" "tools" "stats" "graphics" "grDevices" "utils" "datasets" "methods" "base" other attached packages: YEAST convert marray tkWidgets DynDoc widgetTools arrayMagic genefilter survival vsn affy affyio limma "1.16.0" "1.10.0" "1.14.0" "1.14.0" "1.14.0" "1.12.0" "1.14.0" "1.14.1" "2.31" "2.2.0" "1.14.2" "1.4.1" "2.10.5" Biobase "1.14.1" Yad.

"GHAVI-HELM Yad" <yad.ghavi-helm at="" cea.fr=""> writes: > > > exprsFile<-"D:/exprsData.txt" > exprs<-read.table(exprsFile,header=TRUE,sep="",as.is=TRUE) > > pDataFile<-"D:/pData.txt" > pData<-read.table(pDataFile,header=TRUE, sep="", as.is=TRUE) > > metaData<-"D:/mData.txt" > mData<-read.table(metaData,header=TRUE,sep="",as.is=TRUE) > metData<-new("AnnotatedDataFrame",data=exprs2,varMetadata=mData) > > At this step I have the following error: > Error in `row.names<-.data.frame`(`*tmp*`, value = c("A", "B")) : > length of 'row.names' incorrect > > It seems strangle because "A" and "B" are the colnames of exprsData > (or the rownames of pData). AnnotatedDataFrame coordinates a data.frame with it's metadata. From your naming convention, I'm guessing that what your command is doing is trying to coordinate an expression matrix with its varMetadata. I think what you want to do is > phenoData = new("AnnotatedDataFrame", data=pData, varMetadata=mData) You might then use this to create an ExpressionSet (for example) > new("ExpressionSet", exprs=exprs, phenoData=phenoData) The read.AnnotatedDataFrame page might provide some additional hints on reading data from files; a warning is that read.AnnotatedDataFrame will change (hopefully for the better) in the next release of Bioconductor. Hope that helps, Martin > I tried to do : > > metData<-new("AnnotatedDataFrame",data=exprs2,varMetadata=mData, row.names=1) > > or > > rown=rownames(exprs) > metData<-new("AnnotatedDataFrame",data=exprs2,varMetadata=mData, row.names=rown) > > > but I steel got the same error > > hope anyone could help me... > > >> sessionInfo() > R version 2.5.0 (2007-04-23) > i386-pc-mingw32 > > locale: > LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETAR Y=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252 > > attached base packages: > [1] "tcltk" "splines" "tools" "stats" "graphics" "grDevices" "utils" "datasets" "methods" "base" > > other attached packages: > YEAST convert marray tkWidgets DynDoc widgetTools arrayMagic genefilter survival vsn affy affyio limma > "1.16.0" "1.10.0" "1.14.0" "1.14.0" "1.14.0" "1.12.0" "1.14.0" "1.14.1" "2.31" "2.2.0" "1.14.2" "1.4.1" "2.10.5" > Biobase > "1.14.1" > > > > Yad. > > _______________________________________________ > 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 Bioconductor / Computational Biology http://bioconductor.org