Bioinformatics Advance Access originally published online on October 12, 2007
Bioinformatics 2007 23(23):3170-3177; doi:10.1093/bioinformatics/btm488
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Incorporating prior knowledge of gene functional groups into regularized discriminant analysis of microarray data
Division of Biostatistics, School of Public Health, University of Minnesota, A460 Mayo Building (MMC 303), Minneapolis, MN 55455-0378, USA
*To whom correspondence should be addressed.
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Abstract |
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Motivation: Discriminant analysis for high-dimensional and low-sample-sized data has become a hot research topic in bioinformatics, mainly motivated by its importance and challenge in applications to tumor classifications for high-dimensional microarray data. Two of the popular methods are the nearest shrunken centroids, also called predictive analysis of microarray (PAM), and shrunken centroids regularized discriminant analysis (SCRDA). Both methods are modifications to the classic linear discriminant analysis (LDA) in two aspects tailored to high-dimensional and low-sample-sized data: one is the regularization of the covariance matrix, and the other is variable selection through shrinkage. In spite of their usefulness, there are potential limitations with each method. The main concern is that both PAM and SCRDA are possibly too extreme: the covariance matrix in the former is restricted to be diagonal while in the latter there is barely any restriction. Based on the biology of gene functions and given the feature of the data, it may be beneficial to estimate the covariance matrix as an intermediate between the two; furthermore, more effective shrinkage schemes may be possible.
Results: We propose modified LDA methods to integrate biological knowledge of gene functions (or variable groups) into classification of microarray data. Instead of simply treating all the genes independently or imposing no restriction on the correlations among the genes, we group the genes according to their biological functions extracted from existing biological knowledge or data, and propose regularized covariance estimators that encourages between-group gene independence and within-group gene correlations while maintaining the flexibility of any general covariance structure. Furthermore, we propose a shrinkage scheme on groups of genes that tends to retain or remove a whole group of the genes altogether, in contrast to the standard shrinkage on individual genes. We show that one of the proposed methods performed better than PAM and SCRDA in a simulation study and several real data examples.
Contact: weip{at}biostat.umn.edu
Associate Editor: Joaquin Dopazo
Received on June 5, 2007; revised on August 21, 2007; accepted on September 25, 2007
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