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Detecting Outlier Samples in Microarray Data

Author

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  • Shieh Albert D

    (Harvard University)

  • Hung Yeung Sam

    (University of Hong Kong)

Abstract

In this paper, we address the problem of detecting outlier samples with highly different expression patterns in microarray data. Although outliers are not common, they appear even in widely used benchmark data sets and can negatively affect microarray data analysis. It is important to identify outliers in order to explore underlying experimental or biological problems and remove erroneous data. We propose an outlier detection method based on principal component analysis (PCA) and robust estimation of Mahalanobis distances that is fully automatic. We demonstrate that our outlier detection method identifies biologically significant outliers with high accuracy and that outlier removal improves the prediction accuracy of classifiers. Our outlier detection method is closely related to existing robust PCA methods, so we compare our outlier detection method to a prominent robust PCA method.

Suggested Citation

  • Shieh Albert D & Hung Yeung Sam, 2009. "Detecting Outlier Samples in Microarray Data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 8(1), pages 1-26, February.
    • Handle: RePEc:bpj:sagmbi:v:8:y:2009:i:1:n:13
    DOI: 10.2202/1544-6115.1426
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    References listed on IDEAS

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    1. Lee, Jae Won & Lee, Jung Bok & Park, Mira & Song, Seuck Heun, 2005. "An extensive comparison of recent classification tools applied to microarray data," Computational Statistics & Data Analysis, Elsevier, vol. 48(4), pages 869-885, April.
    2. Zhu, Mu & Ghodsi, Ali, 2006. "Automatic dimensionality selection from the scree plot via the use of profile likelihood," Computational Statistics & Data Analysis, Elsevier, vol. 51(2), pages 918-930, November.
    3. Filzmoser, Peter & Maronna, Ricardo & Werner, Mark, 2008. "Outlier identification in high dimensions," Computational Statistics & Data Analysis, Elsevier, vol. 52(3), pages 1694-1711, January.
    4. 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:

    1. Laura Selicato & Flavia Esposito & Grazia Gargano & Maria Carmela Vegliante & Giuseppina Opinto & Gian Maria Zaccaria & Sabino Ciavarella & Attilio Guarini & Nicoletta Del Buono, 2021. "A New Ensemble Method for Detecting Anomalies in Gene Expression Matrices," Mathematics, MDPI, vol. 9(8), pages 1-26, April.
    2. Junlong Zhao & Chao Liu & Lu Niu & Chenlei Leng, 2019. "Multiple influential point detection in high dimensional regression spaces," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 81(2), pages 385-408, April.
    3. 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.

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