[BioC] agilent bicolor

[Marie-Paule Roth]

Dear All,
Our goal is to localize eQTLs in both the liver and the spleen, using 
200 F2 mice. We thus need to measure gene expression levels in the 
two organs of 200 mice. We are using Agilent 4x44K arrays. For cost 
reasons, I was planning to label liver mRNAs with Cy3 and spleen 
mRNAs with Cy5, hybridize the 2 mRNAs of the same mouse on one array, 
and analyse liver and spleen data separately (eQTLs can differ in 
both organs). Of course, we expect gene expression variability 
between F2 mice, at least for a significant proportion of genes. Is 
there a chance that high gene expression in one organ can influence 
the detected level of fluorescence in the other organ and thus bias 
the results ? If so, is there a way to deal with this problem ?
Thanks a lot for any help and advice.
Marie-Paule