On Mon, Apr 26, 2010 at 9:58 AM, Kalai Vani <kalai_gene@yahoo.co.in> wrote: > Dear Sir, > > I could perform the GEOquery for sample data mentioned in your > PDF, GSE2553 > when I perform the same for another data set 'GSE5764 in GEO > > I get the out put of the sample data set performed before. > > what is my mistake sir. > > gse <- getGEO("GSE5764") > (gse[[1]]) > dat <- exprs(gse[[1]]) > > what should i do if I need to download a new dataset from GEO. > > > *Error* in validObject(.Object) : > invalid class "ExpressionSet" object: featureNames differ between > assayData and featureData > In addition: Warning message: > closing unused connection 3 > (C:\Users\rsgk\AppData\Local\Temp\Rtmp6p5q06/GSE5764_series_matrix.t xt.gz) > > Hello, Kalaivani. This works fine for me using a recent version of GEOquery. Perhaps you need to upgrade, as I think this issue has been fixed. Just as an aside, please be sure to email the bioconductor list, as this gives you the best chance of getting correct answers. Also, be sure to include the output of sessionInfo() with any emails to the list. Sean > gse <- getGEO('GSE5764') Found 1 file(s) GSE5764_series_matrix.txt.gz trying URL ' ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE5764/GSE5764_serie s_matrix.txt.gz ' ftp data connection made, file length 3154972 bytes opened URL ================================================== downloaded 3.0 Mb File stored at: /var/folders/zz/zzzivhrRnAmviuee+++b3E++7lI/-Tmp-//RtmpdfU4SN/GPL570.s oft > gse[[1]] ExpressionSet (storageMode: lockedEnvironment) assayData: 54675 features, 30 samples element names: exprs protocolData: none phenoData sampleNames: GSM134584, GSM134586, ..., GSM134710 (30 total) varLabels and varMetadata description: title: NA geo_accession: NA ...: ... data_row_count: NA (36 total) featureData featureNames: 1007_s_at, 1053_at, ..., AFFX-TrpnX-M_at (54675 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: GPL570 > validObject(gse[[1]]) [1] TRUE > sessionInfo() R version 2.11.0 Under development (unstable) (2009-11-03 r50304) x86_64-apple-darwin locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] GEOquery_2.11.3 RCurl_1.4-1 bitops_1.0-4.1 Biobase_2.7.6 [[alternative HTML version deleted]]