[BioC] Mouse exon array probes

[Richard Williams]

Hello,

We are working on creating a definition file for analyzing a 
mouse genomic array.  We are using the probe sets for the 
Affymetrix GeneChip® Mouse Exon 1.0 ST Array and have 
megablasted the probes against a copy of the most current 
build of the mouse genome (NCBI).  However, some of 
the contigs have very few matches and for 6 contigs, on the 
X chromosome, none at all.  

Has any one else experienced the same while using these 
Affymetrix probes?  Any information or advice will be 
greatly appreciated.

Thanks,
Rick