Probe classification of on-off type DNA microarray images with a nonlinear matching measure

Munho Ryu; Jong Dae Kim; Byoung Goo Min; Jongwon Kim; Y. Y. Kim

doi:10.1117/1.2168166

1 January 2006 Probe classification of on-off type DNA microarray images with a nonlinear matching measure

Munho Ryu, Jong Dae Kim, Byoung Goo Min, Jongwon Kim, Y. Y. Kim

Author Affiliations +

Journal of Biomedical Optics, Vol. 11, Issue 1, 014027 (January 2006). https://doi.org/10.1117/1.2168166

Abstract

We propose a nonlinear matching measure, called counting measure, as a signal detection measure that is defined as the number of on pixels in the spot area. It is applied to classify probes for an on-off type DNA microarray, where each probe spot is classified as hybridized or not. The counting measure also incorporates the maximum response search method, where the expected signal is obtained by taking the maximum among the measured responses of the various positions and sizes of the spot template. The counting measure was compared to existing signal detection measures such as the normalized covariance and the median for 2390 patient samples tested on the human papillomavirus (HPV) DNA chip. The counting measure performed the best regardless of whether or not the maximum response search method was used. The experimental results showed that the counting measure combined with the positional search was the most preferable.

©(2006) Society of Photo-Optical Instrumentation Engineers (SPIE)

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Munho Ryu, Jong Dae Kim, Byoung Goo Min, Jongwon Kim, and Y. Y. Kim "Probe classification of on-off type DNA microarray images with a nonlinear matching measure," Journal of Biomedical Optics 11(1), 014027 (1 January 2006). https://doi.org/10.1117/1.2168166

Published: 1 January 2006

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KEYWORDS

Signal detection

Image classification

Nonlinear optics

Feature selection

Gallium

Medicine

Scatter measurement

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