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

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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. --Naomi 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. > >Sean > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor 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