[BioC] Error in getGEO command with GSEMatrix=TRUE
Marwaha, Shruti (marwahsi)
marwahsi at mail.uc.edu
Wed Mar 13 02:55:49 CET 2013
I am trying to get an ExpressionSet from a GSEfile using getGEO command with GSEMatrix=TRUE. It sometimes gives an error (Connection was reset) if I use GSEMatrix=TRUE however sometimes it works smooth. I have the latest version of R, Bioconductor and GEOquery. Please advise if I am missing some library or need to change some settings. Thanks in advance.
gset <- getGEO("GSE27347", GSEMatrix =TRUE)
Error in function (type, msg, asError = TRUE) :
Send failure: Connection was reset
R version 2.15.2 (2012-10-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
 LC_COLLATE=English_India.1252 LC_CTYPE=English_India.1252
 LC_MONETARY=English_India.1252 LC_NUMERIC=C
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
 limma_3.14.4 GEOquery_2.24.1 Biobase_2.18.0 BiocGenerics_0.4.0
loaded via a namespace (and not attached):
 RCurl_1.95-4.1 tools_2.15.2 XML_3.95-0.2
OS: Windows 7
Methods already attempted
* I have tried it on both RStudio and GUI
* I have also tried using the command "setInternet2(use=FALSE)" but it doesn't help.
* I have tried this command with other GSEfiles also and get the same error.
* GEOquery works fine and downloads the GSEfiles if I give GSEMatrix=FALSE
* I have also tried downloading the file and provide the file path of the file to getGEO with GSEMatrix=TRUE but it does not give an ExpressionSet as output.
Thanks & Regards,
Systems Biology and Physiology
University of Cincinnati
Medical Science Building,
231 Albert Sabin Way
Cincinnati, OH, USA 45267
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