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Nucleic Acids Research Advance Access published online on October 18, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn740
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Computational Biology

A competitive hybridization model predicts probe signal intensity on high density DNA microarrays

Shuzhao Li*, Alex Pozhitkov and Marius Brouwer

Gulf Coast Research Lab, Department of Coastal Sciences, University of Southern Mississippi, Ocean Springs, MS 39564, USA

*To whom correspondence should be addressed: Tel: +1 228 872 4278; Fax: +1 228 872 4204; Email: shuzhao.li{at}gmail.com

Received August 20, 2008. Revised October 1, 2008. Accepted October 2, 2008.

A central, unresolved problem of DNA microarray technology is the interpretation of different signal intensities from multiple probes targeting the same transcript. We propose a competitive hybridization model for DNA microarray hybridization. Our model uses a probe-specific dissociation constant that is computed with current nearest neighbor model and existing parameters, and only four global parameters that are fitted to Affymetrix Latin Square data. This model can successfully predict signal intensities of individual probes, therefore makes it possible to quantify the absolute concentration of targets. Our results offer critical insights into the design and data interpretation of DNA microarrays.


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