[BioC] downloading GEO gds files

[James W. MacDonald]

Hi Dennis,

Wall, Dennis Paul wrote:
> I am trying to download the file gds1917 from GEO using getGEO, but am
> receiving an error
> 
> 
>>library(GEOquery)
> 
> 
>>gds <- getGEO("gds1917")
> 
> 
> trying URL
> 'ftp://ftp.ncbi.nih.gov/pub/geo/data/gds/soft_gz/GDS1917.soft.gz'
> 
> Error in download.file(myurl, destfile, mode = mode) : 
> 
>         cannot open URL
> 'ftp://ftp.ncbi.nih.gov/pub/geo/data/gds/soft_gz/GDS1917.soft.gz'
> 
>  
> 
> it looks like getGEO is looking in the wrong place for the file. The ftp
> address is actually
> 
> ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS1917.soft.gz
> 
>  
> 
> am I doing something wrong?

You didn't give us your sessionInfo(), so I have to fly blind here, but 
I assume you are using an old version of R, and hence an old version of 
GEOquery. URLs are notoriously unstable, so for any package that queries 
a webserver there are often updates that contain the new URL.

 > library(GEOquery)
 > gds <- getGEO("gds1917")
trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS1917.soft.gz'
ftp data connection made, file length 5267985 bytes
opened URL
downloaded 5144Kb

File stored at:
C:\WINDOWS\TEMP\Rtmpy3lkrb/GDS1917.soft.gz
parsing geodata
parsing subsets
ready to return
 > sessionInfo()
R version 2.4.1 (2006-12-18)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] "stats"     "graphics"  "grDevices" "utils"     "datasets" 
"methods"   "base"

other attached packages:
GEOquery
  "1.8.0"

Best,

Jim


> 
>  
> 
> Thank you,
> 
>  
> 
> Dennis
> 
>  
> 
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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