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Modified linear discriminant analysis approaches for classification of high-dimensional microarray data

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  • Xu, Ping
  • Brock, Guy N.
  • Parrish, Rudolph S.

Abstract

Linear discriminant analysis (LDA) is one of the most popular methods of classification. For high-dimensional microarray data classification, due to the small number of samples and large number of features, classical LDA has sub-optimal performance corresponding to the singularity and instability of the within-group covariance matrix. Two modified LDA approaches (MLDA and NLDA) were applied for microarray classification and their performance criteria were compared with other popular classification algorithms across a range of feature set sizes (number of genes) using both simulated and real datasets. The results showed that the overall performance of the two modified LDA approaches was as competitive as support vector machines and other regularized LDA approaches and better than diagonal linear discriminant analysis, k-nearest neighbor, and classical LDA. It was concluded that the modified LDA approaches can be used as an effective classification tool in limited sample size and high-dimensional microarray classification problems.

Suggested Citation

  • Xu, Ping & Brock, Guy N. & Parrish, Rudolph S., 2009. "Modified linear discriminant analysis approaches for classification of high-dimensional microarray data," Computational Statistics & Data Analysis, Elsevier, vol. 53(5), pages 1674-1687, March.
    • Handle: RePEc:eee:csdana:v:53:y:2009:i:5:p:1674-1687
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    1. Ledoit, Olivier & Wolf, Michael, 2004. "A well-conditioned estimator for large-dimensional covariance matrices," Journal of Multivariate Analysis, Elsevier, vol. 88(2), pages 365-411, February.
    2. Duintjer Tebbens, Jurjen & Schlesinger, Pavel, 2007. "Improving implementation of linear discriminant analysis for the high dimension/small sample size problem," Computational Statistics & Data Analysis, Elsevier, vol. 52(1), pages 423-437, September.
    3. Smyth Gordon K, 2004. "Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 3(1), pages 1-28, February.
    4. Parrish, Rudolph S. & Spencer III, Horace J. & Xu, Ping, 2009. "Distribution modeling and simulation of gene expression data," Computational Statistics & Data Analysis, Elsevier, vol. 53(5), pages 1650-1660, March.
    5. Schäfer Juliane & Strimmer Korbinian, 2005. "A Shrinkage Approach to Large-Scale Covariance Matrix Estimation and Implications for Functional Genomics," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 4(1), pages 1-32, November.
    6. Dudoit S. & Fridlyand J. & Speed T. P, 2002. "Comparison of Discrimination Methods for the Classification of Tumors Using Gene Expression Data," Journal of the American Statistical Association, American Statistical Association, vol. 97, pages 77-87, March.
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    Cited by:

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    3. Parrish, Rudolph S. & Spencer III, Horace J. & Xu, Ping, 2009. "Distribution modeling and simulation of gene expression data," Computational Statistics & Data Analysis, Elsevier, vol. 53(5), pages 1650-1660, March.
    4. Kubokawa, Tatsuya & Hyodo, Masashi & Srivastava, Muni S., 2013. "Asymptotic expansion and estimation of EPMC for linear classification rules in high dimension," Journal of Multivariate Analysis, Elsevier, vol. 115(C), pages 496-515.
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    9. Pires, Ana M. & Branco, João A., 2010. "Projection-pursuit approach to robust linear discriminant analysis," Journal of Multivariate Analysis, Elsevier, vol. 101(10), pages 2464-2485, November.
    10. Pedro Duarte Silva, A., 2011. "Two-group classification with high-dimensional correlated data: A factor model approach," Computational Statistics & Data Analysis, Elsevier, vol. 55(11), pages 2975-2990, November.
    11. Ruiyan Luo & Xin Qi, 2017. "Asymptotic Optimality of Sparse Linear Discriminant Analysis with Arbitrary Number of Classes," Scandinavian Journal of Statistics, Danish Society for Theoretical Statistics;Finnish Statistical Society;Norwegian Statistical Association;Swedish Statistical Association, vol. 44(3), pages 598-616, September.
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