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Vol. 20 no. 1 2004, pages 100-104
Bioinformatics © Oxford University Press 2004; all rights reserved.

A generalized likelihood ratio test to identify differentially expressed genes from microarray data

Song Wang * and Stewart Ethier

Department of Mathematics, University of Utah, Salt Lake City, UT 84112, USA

Received on April 3, 2003 ; revised on June 17, 2003 ; accepted on July 26, 2003

Motivation: Microarray technology emerges as a powerful tool in life science. One major application of microarray technology is to identify differentially expressed genes under various conditions. Currently, the statistical methods to analyze microarray data are generally unsatisfactory, mainly due to the lack of understanding of the distribution and error structure of microarray data.

Results: We develop a generalized likelihood ratio (GLR) test based on the two-component model proposed by Rocke and Durbin to identify differentially expressed genes from microarray data. Simulation studies show that the GLR test is more powerful than commonly used methods, like the fold-change method and the two-sample t-test. When applied to microarray data, the GLR test identifies more differentially expressed genes than the t-test, has a lower false discovery rate and shows more consistency over independently repeated experiments.

Availability: The approach is implemented in software called GLR, which is freely available for downloading at http://www.cc.utah.edu/~jw27c60

Contact: song.wang{at}m.cc.utah.edu

* To whom correspondence should be addressed.


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