Probe classification of on-off type DNA microarray images with a nonlinear matching measure.
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.
Ryu
Munho
M
Chonbuk National University, Division of Bionics and Bioinformatics, 664-14 1 Ga, Duckjin-Dong, Duckjin-Gu, Jeonju, Jeonbuk 561-756, South Korea. mhryu@chonbuk.ac.kr
Kim
Jong Dae
JD
Min
Byoung Goo
BG
Kim
Jongwon
J
Kim
Yong-Yook
YY
D001185:Artificial Intelligence; D015344:DNA Probes, HPV / Q000032:analysis* / Q000235:genetics; D004279:DNA, Viral / Q000032:analysis* / Q000235:genetics; D005260:Female; D006801:Humans; D007090:Image Interpretation, Computer-Assisted / Q000379:methods; D008856:Microscopy, Fluorescence / Q000379:methods*; D017711:Nonlinear Dynamics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D030361:Papillomavirus Infections / Q000175:diagnosis* / Q000235:genetics* / Q000821:virology; D010363:Pattern Recognition, Automated / Q000379:methods*; D011230:Precancerous Conditions / Q000175:diagnosis / Q000235:genetics / Q000821:virology; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D002583:Uterine Cervical Neoplasms / Q000175:diagnosis / Q000235:genetics / Q000821:virology
D015344:DNA Probes, HPV; D004279:DNA, Viral