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PLS Dimension Reduction for Classification with Microarray Data

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  • Boulesteix Anne-Laure

    (Department of Statistics, University of Munich)

Abstract

Partial Least Squares (PLS) dimension reduction is known to give good prediction accuracy in the context of classification with high-dimensional microarray data. In this paper, the classification procedure consisting of PLS dimension reduction and linear discriminant analysis on the new components is compared with some of the best state-of-the-art classification methods. Moreover, a boosting algorithm is applied to this classification method. In addition, a simple procedure to choose the number of PLS components is suggested. The connection between PLS dimension reduction and gene selection is examined and a property of the first PLS component for binary classification is proved. In addition, we show how PLS can be used for data visualization using real data. The whole study is based on 9 real microarray cancer data sets.

Suggested Citation

  • Boulesteix Anne-Laure, 2004. "PLS Dimension Reduction for Classification with Microarray Data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 3(1), pages 1-32, November.
    • Handle: RePEc:bpj:sagmbi:v:3:y:2004:i:1:n:33
    DOI: 10.2202/1544-6115.1075
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    Citations

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    Cited by:

    1. González, Javier & Muñoz, Alberto, 2010. "Representing functional data in reproducing Kernel Hilbert Spaces with applications to clustering and classification," DES - Working Papers. Statistics and Econometrics. WS ws102713, Universidad Carlos III de Madrid. Departamento de Estadística.
    2. Florian Rohart & Benoît Gautier & Amrit Singh & Kim-Anh Lê Cao, 2017. "mixOmics: An R package for ‘omics feature selection and multiple data integration," PLOS Computational Biology, Public Library of Science, vol. 13(11), pages 1-19, November.
    3. Schmid Matthias & Hothorn Torsten & Krause Friedemann & Rabe Christina, 2012. "A PAUC-based Estimation Technique for Disease Classification and Biomarker Selection," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(5), pages 1-26, October.
    4. Lê Cao Kim-Anh & Rossouw Debra & Robert-Granié Christèle & Besse Philippe, 2008. "A Sparse PLS for Variable Selection when Integrating Omics Data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 7(1), pages 1-32, November.
    5. Chung Dongjun & Keles Sunduz, 2010. "Sparse Partial Least Squares Classification for High Dimensional Data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 9(1), pages 1-32, March.
    6. Boulesteix Anne-Laure, 2006. "Reader's Reaction to "Dimension Reduction for Classification with Gene Expression Microarray Data" by Dai et al (2006)," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 5(1), pages 1-7, June.
    7. Asuman Turkmen & Nedret Billor, 2013. "Partial least squares classification for high dimensional data using the PCOUT algorithm," Computational Statistics, Springer, vol. 28(2), pages 771-788, April.
    8. Nguyen Tuan S & Rojo Javier, 2009. "Dimension Reduction of Microarray Data in the Presence of a Censored Survival Response: A Simulation Study," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 8(1), pages 1-38, January.

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