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Bioinformatics Advance Access originally published online on April 7, 2005
Bioinformatics 2005 21(12):2803-2804; doi:10.1093/bioinformatics/bti428
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org

Comment on ‘Evaluation of the gene-specific dye bias in cDNA microarray experiments’

Kevin K. Dobbin *, Joanna H. Shih and Richard M. Simon

Biometric Research Branch, National Cancer Institute, National Institutes of Health Bethesda, MD, USA

*To whom correspondence should be addressed.

The first 150 words of the full text of this article appear below.

In their paper in Bioinformatics, Martin-Magniette et al. (2005) recommend complete dye-swap1 designs for both direct and indirect dual label microarray experiments. These recommendations contradict our previous recommendations (Dobbin et al., 2003) for designing experiments, where we suggested minimizing or eliminating the use of dye-swap arrays. We show here that the recommendations of Martin-Magniette et al. are fundamentally flawed, and that in most realistic situations performing extensive dye-swap arrays results in a poor experimental design.

The key error made by these authors is that they focus on over-simplified situations in which only two RNA samples are being compared. There are two problems with this approach. First, if the goal is really just to compare gene expression in two RNA samples, then obviously the best design will be to place aliquots from both samples together on each array and label each sample with each dye . . . [Full Text of this Article]


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