[BioC] Normalization analyzing different strains

[Remo Sanges]

I' m analyzing affymetrix array from 2 different mice strain (C57 and 
SV129).
The strains are genetically different, but I have no numerical value
to descibe this.

Now I' m looking for a suggestion in the normalization strategy.

Basically I would like to know if you judge to be better
to normalize separately the two strains.

Thank you

Remo