On Tue, Mar 12, 2013 at 9:55 PM, Marwaha, Shruti (marwahsi) <
marwahsi@mail.uc.edu> wrote:

> 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
> library(Biobase)
> library(GEOquery)
> library(limma)
> gset <- getGEO("GSE27347", GSEMatrix =TRUE)
>
> Error:
> Error in function (type, msg, asError = TRUE)  :
>   Send failure: Connection was reset
>
>
Hi, Marwaha.

While I cannot be sure, I suspect that these are intermittent connection
problems between you and NCBI.  You could try wrapping your getGEO call in
something like this to catch this condition :

gse = NULL
while(!inherits(gse,'list')) {gse=tryCatch(
  getGEO('GSE27347'),
  error=function(e) {Sys.sleep(5); message('retrying'); return(e)})}

This will continuously retry the getGEO call every 5 seconds until the
outcome is a list, which is what we expect getGEO to return in this case.
 Hopefully, this will make your code a bit more robust.

Sean



> Session Info
>
> > sessionInfo()
>
> R version 2.15.2 (2012-10-26)
>
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
>
>
> locale:
>
> [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
> RAM: 4GB
> 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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