Noise factor analysis for cDNA microarrays

Yoganand Balagurunathan; Naisyin Wang; Edward R. Dougherty; Danh V. Nguyen; Yidong Chen; Michael L. Bittner; Jeffrey M. Trent; Raymond J. Carroll

doi:10.1117/1.1755232

1 July 2004 Noise factor analysis for cDNA microarrays

Yoganand Balagurunathan, Naisyin Wang, Edward R. Dougherty, Danh V. Nguyen, Yidong Chen, Michael L. Bittner, Jeffrey M. Trent, Raymond J. Carroll

Author Affiliations +

Journal of Biomedical Optics, Vol. 9, Issue 4, (July 2004). https://doi.org/10.1117/1.1755232

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.

©(2004) Society of Photo-Optical Instrumentation Engineers (SPIE)

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Yoganand Balagurunathan, Naisyin Wang, Edward R. Dougherty, Danh V. Nguyen, Yidong Chen, Michael L. Bittner, Jeffrey M. Trent, and Raymond J. Carroll "Noise factor analysis for cDNA microarrays," Journal of Biomedical Optics 9(4), (1 July 2004). https://doi.org/10.1117/1.1755232

Published: 1 July 2004

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KEYWORDS

Interference (communication)

Signal to noise ratio

Signal detection

Factor analysis

Statistical analysis

Error analysis

Seaborgium

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