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

[Sean Davis]

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
future.

Sean