[BioC] agilent bicolor
roth at cict.fr
Mon Jan 7 14:45:27 CET 2008
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.
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