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Nucleic Acids Research, 2002, Vol. 30, No. 12 e54
© 2002 Oxford University Press

Microarray optimizations: increasing spot accuracy and automated identification of true microarray signals

Peter H. Tran1,2, Daniel A. Peiffer1, Yongchol Shin1, Lauren M. Meek1, James P. Brody2 and Ken W. Y. Cho1,*

1Department of Developmental and Cell Biology and 2Department of Biomedical Engineering, University of California at Irvine, Irvine, CA 92697, USA

In this paper, fluorescent microarray images and various analysis techniques are described to improve the microarray data acquisition processes. Signal intensities produced by rarely expressed genes are initially correctly detected, but they are often lost in corrections for background, log or ratio. Our analyses indicate that a simple correlation between the mean and median signal intensities may be the best way to eliminate inaccurate microarray signals. Unlike traditional quality control methods, the low intensity signals are retained and inaccurate signals are eliminated in this mean and median correlation. With larger amounts of microarray data being generated, it becomes increasingly more difficult to analyze data on a visual basis. Our method allows for the automatic quantitative determination of accurate and reliable signals, which can then be used for normalization. We found that a mean to median correlation of 85% or higher not only retains more data than current methods, but the retained data is more accurate than traditional thresholds or common spot flagging algorithms. We have also found that by using pin microtapping and microvibrations, we can control spot quality independent from initial PCR volume.

* To whom correspondence should be addressed. Tel: +1 949 824 7950; Fax: +1 949 824 9395; Email: kwcho{at}uci.edu


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