analysing exon arrays with RefSeq ID

[Maria Traka]

Hi,
I am working with mouse exon array data generated from Affy Mouse Exon
1.0 ST Arrays with R/Bioconductor and i want to do some functional
analysis with GenMAPP as i did in the past with human Affy U133Plus
arrays.
I understand that at the moment GenMAPP does not support the Affy
transcript cluster ID for exon arrays so i resorted to using RefSeq
IDs instead. The problem is that when i load my file I get 2527
errors. I have looked at the exceptions file and for these i get an
error message: "Gene not found in RefSeq or any related system. ".
Although some of them are genuine and i can live with that most of
them are not, which i discovered when i searched some RefSeq IDs in
NCBI. I am a bit puzzled by this and not sure how to proceed...
I am using the 'Mm-Std_20070817.gdb' gene database.

Thanks,
Maria

[GenMAPP Support]

Hello Maria,

This is probably due to the GenMAPP database being outdated. We are
currently working on new databases that should be available in a
couple of weeks or in early January.

Regards,

Kristina