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Journal of Biomedical Optics

Probe classification of on-off type DNA microarray images with a nonlinear matching measure
Author(s): Munho Ryu; Jong Dae Kim; Byoung Goo Min; Jongwon Kim; Y. Y. Kim
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Paper 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.

Paper Details

Date Published: 1 January 2006
PDF: 7 pages
J. Biomed. Opt. 11(1) 014027 doi: 10.1117/1.2168166
Published in: Journal of Biomedical Optics Volume 11, Issue 1
Show Author Affiliations
Munho Ryu, Chonbuk National Univ. (South Korea)
Jong Dae Kim, Hallym Univ. (South Korea)
Byoung Goo Min, Seoul National Univ. (South Korea)
Jongwon Kim, BioMedLab Co., Ltd. (South Korea)
Y. Y. Kim, Chonbuk National Univ. (South Korea)

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