[BioC] extracting phenotypic data from GEO (i.e. GSE8671)

[Sean Davis]

On Thu, Jun 4, 2009 at 5:41 PM, Andrew Yee<yee at post.harvard.edu> wrote:
> Hi, I've been working with the GEOquery package.  I'm interested in creating
> a phenotypic data file from GSE8671.  I imagine this should be possible
> after using getGEO(), however, it appears to be taking a substantial amount
> of time to parse through the soft file.  Is there a simpler, quicker method
> of extracting just the phenotypic information?

Hi, Andrew.  You didn't post your sessionInfo(), but in recent
versions of GEOquery, the default is to parse the GSEMatrix files when
getting GSEs.  This is quite a bit faster (typically taking a few
seconds for parsing).

Sean