Hi list, I'm trying to analyse GeneExpressionOmnibus data using the Biobase package. For the GSE record GSE4922 I get an error as shown below, whereas other records (e.g. GSE1456) load without problems. Is there an easy way to fix the problem or get around it? Best Regards, Hendrik > GSE4922 <- getGEO("GSE4922",GSEMatrix=TRUE) Found 4 file(s) GSE4922-GPL96_series_matrix-1.txt.gz trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE4922/GSE4922-GPL9 6_series_matrix-1.txt.gz' ftp data connection made, file length 44890082 bytes opened URL downloaded 42.8 Mb Using locally cached version of GPL96 found here: C:\DOCUME~1\falk\LOCALS~1\Temp\RtmpAjqjX7/GPL96.soft Error in validObject(.Object) : invalid class ?ExpressionSet? object: featureNames differ between assayData and featureData > -- Dr. Hendrik Falk Senior Research Officer High Throughput Chemical Screening Facility The Walter and Eliza Hall Institute of Medical Research Biotechnology Centre 4 Research Avenue Bundoora Victoria 3086 Australia Tel. (+61 3) 9345 2104 Fax. - 2211 Mob. 0420 353572 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}

Hi Hendrick, On 29/02/12 06:46, Hendrik Falk wrote: > Hi list, > > I'm trying to analyse GeneExpressionOmnibus data using the Biobase package. For the > GSE record GSE4922 I get an error as shown below, whereas other records (e.g. > GSE1456) load without problems. Is there an easy way to fix the problem or get > around it? > > Best Regards, > Hendrik > >> GSE4922<- getGEO("GSE4922",GSEMatrix=TRUE) > Found 4 file(s) > GSE4922-GPL96_series_matrix-1.txt.gz > trying URL > 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE4922/GSE4922-GP L96_series_matrix-1.txt.gz' > ftp data connection made, file length 44890082 bytes > opened URL > downloaded 42.8 Mb > > Using locally cached version of GPL96 found here: > C:\DOCUME~1\falk\LOCALS~1\Temp\RtmpAjqjX7/GPL96.soft > Error in validObject(.Object) : > invalid class ?ExpressionSet? object: featureNames differ between assayData and > featureData >> it works on my side (see sessionInfo() below), make sure your packages are up-to-date and that the download was not interrupted. HTH J. > sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets tools methods [8] base other attached packages: [1] GEOquery_2.20.8 Biobase_2.14.0 loaded via a namespace (and not attached): [1] RCurl_1.91-1 XML_3.9-4