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Bioinformatics Advance Access originally published online on April 19, 2005
Bioinformatics 2005 21(13):2994-3000; doi:10.1093/bioinformatics/bti455
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Segmentation of cDNA Microarray Spots Using Markov Random Field Modeling

Omer Demirkaya *, Musa H. Asyali and Mohamed M. Shoukri

Department of Biostatistics, Epidemiology, and Scientific Computing King Faisal Specialist Hospital and Research Center MBC No. 03, PO Box 3354, Riyadh 11211, Saudi Arabia

*To whom correspondence should be addressed.

Motivation: Spot segmentation is a critical step in microarray gene expression data analysis. Therefore, the performance of segmentation may substantially affect the results of subsequent stages of the analysis, such as the detection of differentially expressed genes. Several methods have been developed to segment microarray spots from the surrounding background. In this study, we have proposed a new approach based on Markov random field (MRF) modeling and tested its performance on simulated and real microarray images against a widely used segmentation method based on Mann–Whitney test adopted by QuantArray software (Boston, MA). Spot addressing was performed using QuantArray. We have also devised a simulation method to generate microarray images with realistic features. Such images can be used as gold standards for the purposes of testing and comparing different segmentation methods, and optimizing segmentation parameters.

Results: Experiments on simulated and 14 actual microarray image sets show that the proposed MRF-based segmentation method can detect spot areas and estimate spot intensities with higher accuracy.

Availability: The algorithms were implemented in MatlabTM (The Mathworks, Inc., Natick, MA) environment. The codes for MRF-based segmentation and image simulation methods are available upon request.

Contact: demirkaya{at}ieee.org

Received on December 20, 2004; revised on April 1, 2005; accepted on April 14, 2005

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