failure in GDS2eSet() in package GEOquery
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Wittner, Ben ▴ 290
@wittner-ben-1031
Last seen 5.6 years ago
USA/Boston/Mass General Hospital
Hello, If I execute the following three lines: library('GEOquery') gds <- getGEO('GSE2034') eset <- GDS2eSet(gds) I get the following error message after the call to GDS2eSet(): Error in function (classes, fdef, mtable) : unable to find an inherited method for function "Table", for signature "GSE" I'm using R version 2.6.0 and GEOquery version 2.2.0 (see details below), but it also happens with R version 2.5.2 and GEOquery version 2.0.6. Any help would be appreciated. Thanks. -Ben ---------------------------------------------------------------------- ----- > eset <- GDS2eSet(gds) trying URL 'http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL96&for m=text&vie w=full' Content type 'geo/text' length unknown opened URL .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... (many such lines deleted) .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... ... downloaded 23.4 Mb File stored at: /tmp/Rtmpf1P0of/GPL96.soft Error in function (classes, fdef, mtable) : unable to find an inherited method for function "Table", for signature "GSE" > version _ platform x86_64-unknown-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 2 minor 6.0 year 2007 month 10 day 03 svn rev 43063 language R version.string R version 2.6.0 (2007-10-03) > packageDescription('GEOquery') Package: GEOquery Type: Package Title: Get data from NCBI Gene Expression Omnibus (GEO) Version: 2.2.0 Date: 2007-09-24 Author: Sean Davis <sdavis2 at="" mail.nih.gov=""> Maintainer: Sean Davis <sdavis2 at="" mail.nih.gov=""> Depends: methods,Biobase,RCurl Suggests: limma biocViews: Microarray, DataImport, OneChannel, TwoChannel, SAGE Description: The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data (>150,000 experiments). Given the rich and varied nature of these data, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor. License: GPL version 2 Packaged: Wed Oct 3 14:31:57 2007; biocbuild Built: R 2.6.0; ; 2007-11-05 16:42:50; unix -- File: /home/bwittner/R-2.6.0/library/GEOquery/DESCRIPTION > The information transmitted in this electronic communica...{{dropped:8}}
Microarray OneChannel TwoChannel DataImport bridge GEOquery Microarray OneChannel bridge • 2.5k views
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@saroj-mohapatra-1446
Last seen 6.9 years ago
Hello Ben: >gds <- getGEO('GSE2034') >eset <- GDS2eSet(gds) > >I get the following error message after the call to GDS2eSet(): > >Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "Table", for signature "GSE" > > > Perhaps because 'gds' is not a GDS datastructure (but a GSE datastructure) in this case. From the help page: ----- GDS2eSet(GDS,do.log2=FALSE,GPL=NULL) Arguments GDS The GDS datastructure returned by getGEO ------ Best, Saroj >Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >
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@sean-davis-490
Last seen 14 days ago
United States
Wittner, Ben, Ph.D. wrote: > Hello, > > If I execute the following three lines: > > library('GEOquery') > gds <- getGEO('GSE2034') > eset <- GDS2eSet(gds) Hi, Ben. NCBI GEO nomenclature can be tedious at times. A GSE record is not the same as a GDS record. GDS2eSet() will only work on GDS records, not GSE records. I have made some relatively recent changes to GEOquery to allow loading of GSEMatrix records from GEO. > gseSetList <- getGEO('GSE2034',GSEMatrix=TRUE) > names(gseSetList) [1] "GSE2034_series_matrix-1.txt.gz" "GSE2034_series_matrix-2.txt.gz" It turns out that the GSE is too big for MS Excel (NCBI GEO targeted these files for Excel!), so two files are needed. If you look at either member of the gseSetList, you will see that each is an ExpressionSet that you can simply combine. Hope that helps. Sean
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