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

[Sean Davis]

On Tue, Sep 16, 2008 at 12:35 PM, Robert Gentleman <rgentlem at fhcrc.org> wrote:
>
>
> 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.

Good point, Robert.

I have added GSEMatrix file parsing to the devel version of GEOquery.
It should be available in a day or so after the build system gets
through with it.

Sean