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Bioinformatics Advance Access originally published online on February 22, 2005
Bioinformatics 2005 21(10):2410-2416; doi:10.1093/bioinformatics/bti341
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Background correction for cDNA microarray images using the TV+L1 model

Wotao Yin 1,3,*, Terrence Chen 2,3, Sean Xiang Zhou 3 and Amit Chakraborty 3

1Department of Industrial Engineering and Operations Research, Columbia University New York, NY 10027, USA
2Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign Urbana, IL 61801, USA
3Siemens Corporate Research, Inc. Princeton, NJ 08540, USA

*To whom correspondence should be addressed.

Motivation: Background correction is an important preprocess in cDNA microarray data analysis. A variety of methods have been used for this purpose. However, many kinds of backgrounds, especially inhomogeneous ones, cannot be estimated correctly using any of the existing methods. In this paper, we propose the use of the TV+L1 model, which minimizes the total variation (TV) of the image subject to an L1-fidelity term, to correct background bias. We demonstrate its advantages over the existing methods by both analytically discussing its properties and numerically comparing it with morphological opening.

Results: Experimental results on both synthetic data and real microarray images demonstrate that the TV+L1 model gives the restored intensity that is closer to the true data than morphological opening. As a result, this method can serve an important role in the preprocessing of cDNA microarray data.

Contact: wy2002{at}columbia.edu


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