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Joint adaptive mean–variance regularization and variance stabilization of high dimensional data

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  • Dazard, Jean-Eudes
  • Sunil Rao, J.

Abstract

The paper addresses a common problem in the analysis of high-dimensional high-throughput “omics” data, which is parameter estimation across multiple variables in a set of data where the number of variables is much larger than the sample size. Among the problems posed by this type of data are that variable-specific estimators of variances are not reliable and variable-wise tests statistics have low power, both due to a lack of degrees of freedom. In addition, it has been observed in this type of data that the variance increases as a function of the mean. We introduce a non-parametric adaptive regularization procedure that is innovative in that (i) it employs a novel “similarity statistic”-based clustering technique to generate local-pooled or regularized shrinkage estimators of population parameters, (ii) the regularization is done jointly on population moments, benefiting from C. Stein’s result on inadmissibility, which implies that usual sample variance estimator is improved by a shrinkage estimator using information contained in the sample mean. From these joint regularized shrinkage estimators, we derived regularized t-like statistics and show in simulation studies that they offer more statistical power in hypothesis testing than their standard sample counterparts, or regular common value-shrinkage estimators, or when the information contained in the sample mean is simply ignored. Finally, we show that these estimators feature interesting properties of variance stabilization and normalization that can be used for preprocessing high-dimensional multivariate data. The method is available as an R package, called ‘MVR’ (‘Mean–Variance Regularization’), downloadable from the CRAN website.

Suggested Citation

  • Dazard, Jean-Eudes & Sunil Rao, J., 2012. "Joint adaptive mean–variance regularization and variance stabilization of high dimensional data," Computational Statistics & Data Analysis, Elsevier, vol. 56(7), pages 2317-2333.
    • Handle: RePEc:eee:csdana:v:56:y:2012:i:7:p:2317-2333
    DOI: 10.1016/j.csda.2012.01.012
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    References listed on IDEAS

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    1. Tong, Tiejun & Wang, Yuedong, 2007. "Optimal Shrinkage Estimation of Variances With Applications to Microarray Data Analysis," Journal of the American Statistical Association, American Statistical Association, vol. 102, pages 113-122, March.
    2. Ishwaran H. & Rao J.S., 2003. "Detecting Differentially Expressed Genes in Microarrays Using Bayesian Model Selection," Journal of the American Statistical Association, American Statistical Association, vol. 98, pages 438-455, January.
    3. Robert Tibshirani & Guenther Walther & Trevor Hastie, 2001. "Estimating the number of clusters in a data set via the gap statistic," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 63(2), pages 411-423.
    4. 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.
    5. Youngchao Ge & Sandrine Dudoit & Terence Speed, 2003. "Resampling-based multiple testing for microarray data analysis," TEST: An Official Journal of the Spanish Society of Statistics and Operations Research, Springer;Sociedad de Estadística e Investigación Operativa, vol. 12(1), pages 1-77, June.
    6. Yuedong Wang & Yanyuan Ma & Raymond J. Carroll, 2009. "Variance estimation in the analysis of microarray data," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 71(2), pages 425-445, April.
    7. John D. Storey & Jonathan E. Taylor & David Siegmund, 2004. "Strong control, conservative point estimation and simultaneous conservative consistency of false discovery rates: a unified approach," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 66(1), pages 187-205, February.
    8. Ishwaran, Hemant & Rao, J. Sunil, 2005. "Spike and Slab Gene Selection for Multigroup Microarray Data," Journal of the American Statistical Association, American Statistical Association, vol. 100, pages 764-780, September.
    9. John D. Storey, 2007. "The optimal discovery procedure: a new approach to simultaneous significance testing," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 69(3), pages 347-368, June.
    10. Jianqing Fan & Jinchi Lv, 2008. "Sure independence screening for ultrahigh dimensional feature space," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 70(5), pages 849-911, November.
    11. Efron B. & Tibshirani R. & Storey J.D. & Tusher V., 2001. "Empirical Bayes Analysis of a Microarray Experiment," Journal of the American Statistical Association, American Statistical Association, vol. 96, pages 1151-1160, December.
    12. Christopher Genovese & Larry Wasserman, 2002. "Operating characteristics and extensions of the false discovery rate procedure," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 64(3), pages 499-517, August.
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