[BioC] call of differential expression between close species using microarray data

[pkuonline]

Hi list members,

I'd like to call differential expression between close species (mouse and rat) using microarray data. In other words, I hope to identify orthologous genes with significant expressional differences. 

I know for one species people usually normalize microarray data using RMA (or GCRMA) and then call differential expression using LIMMA. Now, in my case, I am wondering how to do such a cross-species (platform) analysis. First of all, it seems I could not normalize these samples together since they have different CDF files. Second, if I normalize them separately, I am not sure whether these two datasets are comparable. After all, for one ortholog, the mouse probes and rat probes might be different and thus tend to generate different fluorescent intensity. 

Does anyone know how to analyze this cross-platform expressional divergence?

Many thanks ahead.
 				
Best regards,
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Yong Zhang
Ph.D, Research Scholar
Manyuan Long's Lab
University of Chicago