[BioC] agilent bicolor

Naomi Altman naomi at stat.psu.edu
Mon Jan 7 15:30:08 CET 2008

Usually a dye-balance design is used.  In half the samples, liver is 
labeled with Cy3 and in half, spleen is labeled with Cy3.  Otherwise, 
proceed as you have suggested.

This guards against gene-specific dye bias.


At 09:08 AM 1/7/2008, Sean Davis wrote:
>On Jan 7, 2008 8:45 AM, Marie-Paule Roth <roth at cict.fr> wrote:
> > 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 ?
> >
>We have done this sort of thing using Agilent Tiling arrays and have not
>seen a significant problem with that approach.
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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