On Mon, Sep 8, 2008 at 3:08 PM, hemant ritturaj <ritturajhemant at="" gmail.com=""> wrote: > Dear Sean > > Thanks for the reply > > I tried the way you have suggested but again it gave me an error > > gse6901.eset <- getGEO("GSE6901")[[1]] > > > Error in validObject(.Object) : > invalid class "ExpressionSet" object: featureNames differ between > assayData and featureData > > Check the version of R and other packges which are updated to newer version Hemant, I'm not sure what the problem is. This works fine for me (see sessionInfo below). If you quit R and restart it with an empty workspace and execute the following, do you get the same error? Sean ---------------------------------------------------- > library(GEOquery) > gse <- getGEO('gse6901')[[1]] > gse ExpressionSet (storageMode: lockedEnvironment) assayData: 57381 features, 12 samples element names: exprs phenoData sampleNames: GSM159259, GSM159260, ..., GSM159270 (12 total) varLabels and varMetadata description: title: NA geo_accession: NA ...: ... data_row_count: NA (35 total) featureData featureNames: AFFX-BioB-3_at, AFFX-BioB-5_at, ..., RPTR-Os- XXU09476-1_a t (57381 total) fvarLabels and fvarMetadata description: ID: NA GB_ACC: NA ...: ... Gene.Ontology.Molecular.Function: NA (16 total) additional fvarMetadata: Column, Description experimentData: use 'experimentData(object)' Annotation: GPL2025 > sessionInfo() R version 2.7.2 (2008-08-25) i386-apple-darwin8.11.1 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GEOquery_2.4.5 RCurl_0.9-4 Biobase_2.0.1 --------------------------------------------------------- > On Tue, Sep 9, 2008 at 12:52 AM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >> >> On Mon, Sep 8, 2008 at 2:37 PM, hemant ritturaj >> <ritturajhemant at="" gmail.com=""> wrote: >> > Dear all, >> > >> > I was trying to make expression set from the GSE data >> >> This will get you an ExpressionSet: >> >> gse6901.eset <- getGEO("GSE6901")[[1]] >> >> Now, gse6901.eset is an ExpressionSet. No need for all the code >> below. The [[1]] is needed because getGEO() on a GSEMatrix returns a >> list of ExpressionSets. In this particular case, there is only one >> ExpressionSet, so we choose it. >> >> Sean >> >> > Following is the code >> > >> > gse6901 <- getGEO("GSE6901", GSEMatrix=F) >> > probesets <- Table(GPLList(gse6901)[[1]])$ID >> > data.matrix <- log2(do.call("cbind", lapply(GSMList(gse6901), >> > function(x) { >> > + tab <- Table(x) >> > + mymatch <- match(probesets, tab$ID_REF) >> > + return(as.numeric(tab$VALUE[mymatch])) >> > + }))) >> > rownames(data.matrix) <- probesets >> > colnames(data.matrix) <- names(GSMList(gse6901)) >> > pdata <- data.frame(samples = names(GSMList(gse6901))) >> > rownames(pdata) <- names(GSMList(gse6901)) >> > pheno <- new("phenoData", pData = pdata, varLabels = as.list("samples")) >> > >> > >> > Error: The phenoData class is defunct, use AnnotatedDataFrame (with >> > ExpressionSet) instead >> > >> > I am not able to understand what function has exactly gor changed in >> > Biobase >> > module as I tried >> > >> > pheno <- new("AnnotatedDataFrame", pData = pdata, varLabels = >> > as.list("samples")) >> > >> > then again got an error >> > >> > Error in .nextMethod(.Object, ...) : >> > invalid names for slots of class "AnnotatedDataFrame": pData, varLabels >> > >> > Kindly anyone please help me sorting out this error, I shall be very >> > thankful for your kind help >> > >> > Regards >> > -- >> > Hemant Ritturaj Kushwaha >> > >> > [[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 >> > > > > >