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A mixture factor model with applications to microarray data

Author

Listed:
  • Chaofeng Yuan

    (Northeast Normal University)

  • Wensheng Zhu

    (Northeast Normal University)

  • Xuming He

    (University of Michigan)

  • Jianhua Guo

    (Northeast Normal University)

Abstract

Investigators routinely use unidimensional summaries for multidimensional data. In microarray data analysis, for example, the gene expression level is indeed a unidimensional summary of probe-level or SNP measurements. In this paper, we propose a mixture factor model for the low-level data, which enables us to examine the adequacy of a unidimensional summary while accommodating known or latent subgroups in the population. We also develop screening procedures based on the proposed model to identify potentially informative genes in biomedical studies. As shown in our empirical studies, the proposed methods are often more effective than existing methods because the new model goes beyond the conventional unidimensional summaries of gene expressions.

Suggested Citation

  • Chaofeng Yuan & Wensheng Zhu & Xuming He & Jianhua Guo, 2019. "A mixture factor model with applications to microarray data," TEST: An Official Journal of the Spanish Society of Statistics and Operations Research, Springer;Sociedad de Estadística e Investigación Operativa, vol. 28(1), pages 60-76, March.
    • Handle: RePEc:spr:testjl:v:28:y:2019:i:1:d:10.1007_s11749-018-0585-3
    DOI: 10.1007/s11749-018-0585-3
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    References listed on IDEAS

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    1. McLachlan, G.J. & Bean, R.W. & Ben-Tovim Jones, L., 2007. "Extension of the mixture of factor analyzers model to incorporate the multivariate t-distribution," Computational Statistics & Data Analysis, Elsevier, vol. 51(11), pages 5327-5338, July.
    2. Yiu-Fai Yung, 1997. "Finite mixtures in confirmatory factor-analysis models," Psychometrika, Springer;The Psychometric Society, vol. 62(3), pages 297-330, September.
    3. Hu, Jianhua & Wright, Fred A. & Zou, Fei, 2006. "Estimation of Expression Indexes for Oligonucleotide Arrays Using the Singular Value Decomposition," Journal of the American Statistical Association, American Statistical Association, vol. 101, pages 41-50, March.
    4. Lawrence Hubert & Phipps Arabie, 1985. "Comparing partitions," Journal of Classification, Springer;The Classification Society, vol. 2(1), pages 193-218, December.
    5. Chen, Jiahua & Tan, Xianming, 2009. "Inference for multivariate normal mixtures," Journal of Multivariate Analysis, Elsevier, vol. 100(7), pages 1367-1383, August.
    6. Lin, Tsung-I & McLachlan, Geoffrey J. & Lee, Sharon X., 2016. "Extending mixtures of factor models using the restricted multivariate skew-normal distribution," Journal of Multivariate Analysis, Elsevier, vol. 143(C), pages 398-413.
    7. Murray, Paula M. & Browne, Ryan P. & McNicholas, Paul D., 2014. "Mixtures of skew-t factor analyzers," Computational Statistics & Data Analysis, Elsevier, vol. 77(C), pages 326-335.
    8. 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.
    9. Cristina Tortora & Paul D. McNicholas & Ryan P. Browne, 2016. "A mixture of generalized hyperbolic factor analyzers," Advances in Data Analysis and Classification, Springer;German Classification Society - Gesellschaft für Klassifikation (GfKl);Japanese Classification Society (JCS);Classification and Data Analysis Group of the Italian Statistical Society (CLADAG);International Federation of Classification Societies (IFCS), vol. 10(4), pages 423-440, December.
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