[BioC] problems about cDNA vs genomic arrays normalization

[yanju]

Dear all,

I have got a microarray dataset derived from common reference design. 
The common reference is gemoic DNA.  In normal normalization, we assume 
that  large fraction of genes is not differently expressed, then the 
adjustment strategies are used to let the log-ratios have a median(mean) 
of 0. But in my case, every spot would have the same observed signal in 
the genomic channel while the signals in the cDNA channel vary greatly. 
Therefore, the strategies that i just mentioned are not suitable. I was 
wondering how to normalize this kinds of data? Is that any packages or 
functions existed already? Expecting your reply.

Regards,
Yanju