On Sun, Jul 26, 2009 at 7:55 AM, Aleš Maver <ales.maver@gmail.com> wrote:

> DeaR bioconductors,
> I am trying to process results for some Illumina datasets obtained
> from GEO repository (with geoquery). Usually signals from illumina
> arrays are filtered using detection score p-value. I can see that
> these score values are available on the GEO webpage, however I do not
> know where (if it all) these values are stored in the ExpressionSets
> obtained with the getGEO function.
> Any help on this or advice on alternatives to filter illumina data
> with detection scores are appreciated in advance!
>

Hi, Ales.  The ExpressionSet will not have the p-values for detection
included unless you use getGEO with the parameter GSEMatrix=FALSE and then
construct the ExpressionSet yourself.  There is an example of doing so in
the vignette, but you will need to change the details to match the situation
at hand.  If there is raw data available for your dataset, you could try
using that instead (with lumi or beadarray packages, as an example) and
combine it with the phenodata from the downloaded ExpressionSet.

Sean

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