[BioC] Filtering genes in illumina datasets obtained with GEOquery

James F. Reid james.reid at ifom-ieo-campus.it
Sun Jul 26 15:01:06 CEST 2009

Hi Ales,

suppose that the ExpressionSet returned by GEOquery is called eset, then 
dims(eset) will return the dimensions of all the members of the 
assayData of eset, which will contain exprs (default) and then maybe 
some other matrices say exprs.se which you can access with 
assayData(eset)$exprs.se (if that is indeed the name of the matrix).


Aleš Maver 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!
> Have a nice day,
> Aleš Maver
> Ales.Maver at gmail.com
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