[BioC] Error in getGEO command with GSEMatrix=TRUE

Marwaha, Shruti (marwahsi) marwahsi at mail.uc.edu
Wed Mar 13 02:55:49 CET 2013

Dear Developers,

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.

My Code
gset <- getGEO("GSE27347", GSEMatrix =TRUE)

Error in function (type, msg, asError = TRUE)  :
  Send failure: Connection was reset

Session Info

> sessionInfo()

R version 2.15.2 (2012-10-26)

Platform: x86_64-w64-mingw32/x64 (64-bit)


[1] LC_COLLATE=English_India.1252  LC_CTYPE=English_India.1252

[3] LC_MONETARY=English_India.1252 LC_NUMERIC=C

[5] LC_TIME=English_India.1252

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:

[1] limma_3.14.4       GEOquery_2.24.1    Biobase_2.18.0     BiocGenerics_0.4.0

loaded via a namespace (and not attached):

[1] RCurl_1.95-4.1 tools_2.15.2   XML_3.95-0.2

System Properties
OS: Windows 7
Processor: 2GHz

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,
Shruti Marwaha

Graduate Student
Systems Biology and Physiology
University of Cincinnati
Medical Science Building,
231 Albert Sabin Way
Cincinnati, OH, USA 45267

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