[BioC] Affy Exon arrays

[Tarca, Adi]

Hi all,
I was wondering if there is any method implemented in bioconductor for the analysis of Affymetrix Exon Arrays.
I used the exonmap package & affy tools to get RMA summarized expression values, but there are aboud 1.4 milions probesets, 
which is a bit too much to test while controling the FDR.
Is there a way to get a gene level index so that I can test about 20 000 genes rather than 1.4 milion probestes. I am not interested in alternative splicing but in gene expression.

Thanks,
Adi