[BioC] GEOquery - was queryGEO fails on GDS files (GEO Datasets)
bioconductor-mailinglist at maubp.freeserve.co.uk
Wed Jan 4 17:25:30 CET 2006
Sean Davis wrote:
> I have recently uploaded a new package to bioconductor called GEOquery.
Very recently! I was scouring the net for something like this before
Christmas, but to no avail.
I'm particularly interested in your function GDS2eSet for turning a GDS
file into a standard BioConductor exprSet object.
I managed to cobble together something similar using a combination of
BioPython's GEO parser and rpy (R from Python) as an experiment over
I'm going to have a closer look at if/how you expose the subsample
information in the exprSet phenoData.
> It is available as a development package
> (http://www.bioconductor.org/packages/bioc/1.8/html/GEOquery.html), but it
> doesn't depend on much, so should work with recent R and bioconductor
> releases. It is capable of downloading and parsing GDS, GSM, GPL, and GSE.
> (GSE download and parsing seems to be broken on windows, at least for some
> GSEs--working on that). After installing, you could do:
I see there is a source bundle online (file GEOquery_1.5.1.tar.gz) but
as yet no Windows binary. Is this something you could provide?
Alternatively, how would I compile this myself? I do have MSVC 6.0
In the meantime, I'll try and have a go at home on my linux box...
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