On Tue, Oct 26, 2010 at 5:38 AM, Daniel Brewer <daniel.brewer@icr.ac.uk>wrote:

> Hello,
>
> For a particular GSE set I have downloaded all the raw data but I would
> like to be able to extract all the phenodata associated with each sample
> into a table so I can use it in the analysis.  4.1 of the manual shows a
> way of getting what I want but I would have to download the whole GSE
> matrix.  Is there a way of getting just the meta data?
>
>
Hi, Dan.  The best way is to use getGEO() on the GSE and then extract the
phenoData object from that.  I know that means downloading the entire GSE
Matrix file since partial GSE Matrix files are not available.  I had toyed
with getting partial SOFT format output early on in GEOquery development,
but I didn't complete that work as it required working with the web form and
that felt a little unsafe for maintenance.

Note that a few GSEs are now including separate data tables with the sample
annotation.  These can be downloaded using the getGSEDataTables() function.


Sean

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