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Journal of Biomedical Optics

Noise factor analysis for cDNA microarrays
Author(s): Yoganand Balagurunathan; Naisyin Wang; Edward R. Dougherty; Danh V. Nguyen; Yidong Chen; Michael L. Bittner; Jeffrey M. Trent; Raymond J. Carroll
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Paper Abstract

A microarray-image model is used that takes into account many factors, including spot morphology, signal strength, background fluorescent noise, and shape and surface degradation. The model yields synthetic images whose appearance and quality reflect that of real microarray images. The model is used to link noise factors to the fidelity of signal extraction with respect to a standard image-extraction algorithm. Of particular interest is the identification of the noise factors and their interactions that significantly degrade the ability to accurately detect the true gene-expression signal. This study uses statistical criteria in conjunction with the simulation of various noise conditions to better understand the noise influence on signal extraction for cDNA microarray images. It proposes a paradigm that is implemented in software. It specifically considers certain kinds of noise in the noise model and sets these at certain levels; however, one can choose other types of noise or use different noise levels. In sum, it develops a statistical package that can work in conjunction with the existing image simulation toolbox.

Paper Details

Date Published: 1 July 2004
PDF: 16 pages
J. Biomed. Opt. 9(4) doi: 10.1117/1.1755232
Published in: Journal of Biomedical Optics Volume 9, Issue 4
Show Author Affiliations
Yoganand Balagurunathan, TGEN (United States)
Naisyin Wang, Texas A&M Univ. (United States)
Edward R. Dougherty, Texas A&M Univ. (United States)
Danh V. Nguyen, Texas A&M Univ. (United States)
Yidong Chen, National Institutes of Health (United States)
Michael L. Bittner, National Institutes of Health (United States)
Jeffrey M. Trent, National Institutes of Health (United States)
Raymond J. Carroll, Texas A&M Univ. (United States)

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