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Bioinformatics Advance Access originally published online on September 16, 2004
Bioinformatics 2005 21(5):644-649; doi:10.1093/bioinformatics/bti036
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Reliability analysis of microarray data using fuzzy c-means and normal mixture modeling based classification methods

Musa H. Asyali 1,* and Musa Alci 2

1 Department of Biostatistics, Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Center PO Box 3354, MBC-03, Riyadh 11211, Saudi Arabia
2 Department of Electrical and Electronics Engineering, Ege University Bornova, Izmir 35100, Turkey

*To whom correspondence should be addressed.

Motivation: A serious limitation in microarray analysis is the unreliability of the data generated from low signal intensities. Such data may produce erroneous gene expression ratios and cause unnecessary validation or post-analysis follow-up tasks. Therefore, the elimination of unreliable signal intensities will enhance reproducibility and reliability of gene expression ratios produced from microarray data. In this study, we applied fuzzy c-means (FCM) and normal mixture modeling (NMM) based classification methods to separate microarray data into reliable and unreliable signal intensity populations.

Results: We compared the results of FCM classification with those of classification based on NMM. Both approaches were validated against reference sets of biological data consisting of only true positives and true negatives. We observed that both methods performed equally well in terms of sensitivity and specificity. Although a comparison of the computation times indicated that the fuzzy approach is computationally more efficient, other considerations support the use of NMM for the reliability analysis of microarray data.

Availability: The classification approaches described in this paper and sample microarray data are available as Matlab TM (The MathWorks Inc., Natick, MA) programs (mfiles) and text files, respectively, at http://rc.kfshrc.edu.sa/bssc/staff/MusaAsyali/Downloads.asp. The programs can be run/tested on many different computer platforms where Matlab is available.

Contact: asyali{at}kfshrc.edu.sa


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