[BioC] troubles with GEOquery
sdavis2 at mail.nih.gov
Sat May 10 14:15:23 CEST 2008
2008/5/10 Pascal Barbry <barbry at ipmc.cnrs.fr>:
> Hello Sean,
> Sorry about that! The SOFT file seems correctly downloaded, then the
> processor works full speed for hours (parsing the file???), and I am loosing
> the access to the R console. I left once overnight and nothing better
> happened. This is why I was unable to send error messages. I will re-run the
> same command and I will forward them to you.
Is there a reason to not use GSEMatrix=TRUE? That will be
significantly faster. Over a wireless, it takes about 30 seconds.
When parsing the entire SOFT file, it could take several hours. I
noticed that there are supplementary .CEL files available, also. You
could use getGEOSuppFiles() to download those and process them local
using Bioconductor tools.
Let me know if you have further questions.
> Sean Davis a écrit :
>> On Fri, May 9, 2008 at 6:34 PM, Pascal Barbry <barbry at ipmc.cnrs.fr> wrote:
>>> Hi all,
>>> I have troubles trying to download GSE files from GEO:
>>> GSE6281 <- getGEO("GSE6281", GSEMatrix = FALSE).
>>> Surprisingly, the example found in the help file is working nicely:
>>> gse <- getGEO("GSE462", GSEMatrix = FALSE)
>>> My troubles started after switching to the new version of Bioconductor.
>>> As I
>>> am using a Windows OS and that some of the getGEO options are not
>>> windows-proof, I was wondering if any others had experienced a similar
>>> situation? Any idea (outside swtching to Linux) would be appreciated.
>> Hi, Pascal. What problems are you having? You didn't give a report
>> of the errors that you received.
>>> R version 2.7.0 (2008-04-22)
>>> attached base packages:
>>>  tools stats graphics grDevices utils datasets methods
>>>  base
>>> other attached packages:
>>>  GEOquery_2.4.0 RCurl_0.9-2 Biobase_2.0.1
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
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>>> Release Date: 09/05/2008 12:38
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