[BioC] GEOQuery - from a LOCAL SOFT file to an ExprSet object

[Robert Gentleman]

Sean Davis wrote:
> On Tue, Sep 16, 2008 at 8:33 AM, michael watson (IAH-C)
> <michael.watson at bbsrc.ac.uk> wrote:
>> Dear All
>>
>> Having read the GEOQuery documentation, there are commands which fetch
>> SERIES files from the web and convert to ExprSet, and there are commands
>> that take a GDS and convert to ExprSet - however, for some reason, my R
>> connection to NCBI works only in about 20% of cases - connections to all
>> other websites are fine - and I simply want to get the file myself (SOFT
>> or SERIES, I don't mind), store it locally and open it in getGEO and
>> convert to an ExprSet object.
>>
>> Is that possible?
> 
> With everything except GSEMatrix, it is possible.  See the filename
> argument in getGEO.  I am adding GSEMatrix file parsing in the near

   With the proviso that it is ExpressionSet's that are wanted. 
ExprSet's are deprecated.


> future.
> 
> Sean
> 
> _______________________________________________
> 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
> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org