Skip Navigation



Bioinformatics Advance Access published online on April 19, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti455
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
21/13/2994    most recent
bti455v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Demirkaya, O.
Right arrow Articles by Shoukri, M. M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Demirkaya, O.
Right arrow Articles by Shoukri, M. M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received December 20, 2004
Revised April 1, 2005
Accepted April 14, 2005

Article

Segmentation of microarray cDNA spots using Markov random field modeling

Omer Demirkaya 1*, Musa H. Asyali 1, and Mohamed M. Shoukri 1

1 Department of Biostatistics, Epidemiology, and Scientific Computing, King Faisal Specialist Hospital and Research Center, Riyadh, 11211, Saudi Arabia

* To whom correspondence should be addressed.
Omer Demirkaya, E-mail: demirkaya{at}ieee.org


  Abstract

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.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
A. Daskalakis, D. Cavouras, P. Bougioukos, S. Kostopoulos, D. Glotsos, I. Kalatzis, G. C. Kagadis, C. Argyropoulos, and G. Nikiforidis
Improving gene quantification by adjustable spot-image restoration
Bioinformatics, September 1, 2007; 23(17): 2265 - 2272.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J. Baek, Y. S. Son, and G. J. McLachlan
Segmentation and intensity estimation of microarray images using a gamma-t mixture model
Bioinformatics, February 15, 2007; 23(4): 458 - 465.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
A. Lehmussola, P. Ruusuvuori, and O. Yli-Harja
Evaluating the performance of microarray segmentation algorithms
Bioinformatics, December 1, 2006; 22(23): 2910 - 2917.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.