[BioC] GEOquery downloading problems

[michael watson (IAH-C)]

Set http_proxy and ftp_proxy using Sys.putenv()
Also, unset no_proxy if using linux.


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch on behalf of Sean Davis
Sent: Wed 12/12/2007 12:58 PM
To: Bruce Tabor
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] GEOquery downloading problems
 
On Dec 12, 2007 2:03 AM, Bruce Tabor <BTabor at ccia.unsw.edu.au> wrote:

> Dear BioC crew - especially Sean,
>
> I'm a newbie to R and Bioconductor. I've just started looking a
> microarray data.
>
> I've had a few problems downloading GEO data with GEOquery.
>
> My source data is here:
> http://www.ncbi.nlm.nih.gov/projects/geo/gds/gds_browse.cgi?gds=1816
>
> Here's the code:
> > gse4271<-getGEO("GSE4271")
> trying URL
> 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/by_series/GSE4271/GSE4271_fami
> ly.soft.gz'
> Error in download.file(myurl, destfile, mode = mode) :
>  cannot open URL
> 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/by_series/GSE4271/GSE4271_fami
> ly.soft.gz'
> In addition: Warning message:
> In download.file(myurl, destfile, mode = mode) :
>  failed to create a data connection
>
> > gds1816<-getGEO("GSE1816")
> trying URL
> 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/by_series/GSE1816/GSE1816_fami
> ly.soft.gz'
> Error in download.file(myurl, destfile, mode = mode) :
>  cannot open URL
> 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/by_series/GSE1816/GSE1816_fami
> ly.soft.gz'
> In addition: Warning message:
> In download.file(myurl, destfile, mode = mode) :
>  failed to create a data connection
> >
>
> Other datasets are not working either:
> > gds <- getGEO("GDS1")
> trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS1.soft.gz'
> Error in download.file(myurl, destfile, mode = mode) :
>  cannot open URL
> 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS1.soft.gz'
> In addition: Warning message:
> In download.file(myurl, destfile, mode = mode) :
>  failed to create a data connection
> >
>
> Although sample data appears to be working:
> > gsm97138 <- getGEO("GSM97138")
> trying URL
> 'http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GSM97138&fo
> rm=text&view=full'
> Content type 'geo/text' length unknown
> opened URL
> downloaded 377 Kb
>
> File stored at:
> C:\DOCUME~1\btabor\LOCALS~1\Temp\RtmpsW3lE1/GSM97138.soft
> >
>
> Unfortunately I don't want raw data at this stage.
>

This won't get you raw data, either--at least not in all cases.  A GSE
record is a concatenation of the GSM records.  A GSEMatrix record is simply
the "VALUE" column from each GSE record in a single table.


>
> Session info is:
>
> > sessionInfo()
> R version 2.6.0 (2007-10-03)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MON
> ETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
> [1] GEOquery_2.2.0 RCurl_0.8-1    Biobase_1.16.1
> >
>
> PS. I'm running R off an external drive as my network privileges wont
> let me put it on my C-drive:
> E:\R-2.6.0\bin
> E:\R-2.6.0\library\GEOquery
>

Running off an external drive probably isn't the problem.  This looks like a
proxy problem, especially since the http:// download to get a sample works
(note that I think it is the fact that http:// is used, not the fact that
you are trying to retrieve a sample).  So, you will need to see if you can
set up a proxy for ftp connections.  You might start with the help for
download.file() for how to do that, but you may also need to contact your
computer support staff for some assistance.

Hope that helps.

Sean

	[[alternative HTML version deleted]]

_______________________________________________
Bioconductor mailing list
Bioconductor at stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor