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Assumption adequacy averaging as a concept for developing more robust methods for differential gene expression analysis

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  • Pounds, Stan
  • Rai, Shesh N.

Abstract

The concept of assumption adequacy averaging is introduced as a technique for developing more robust methods that incorporate assessments of assumption adequacy into the analysis. The concept is illustrated by using it to develop a method that averages results from the t-test and nonparametric rank-sum test with weights obtained from using the Shapiro-Wilk test to test the assumption of normality. Through this averaging process, the proposed method is able to rely more heavily on the statistical test that the data suggests is superior for each individual gene. Subsequently, this method developed by assumption adequacy averaging outperforms its two component methods (the t-test and rank-sum test) in a series of traditional and bootstrap-based simulation studies. The proposed method showed greater concordance in gene selection across two studies of gene expression in acute myeloid leukemia than did the t-test or rank-sum test. An R routine for implementing the method is available from www.stjuderesearch.org/depts/biostats.

Suggested Citation

  • Pounds, Stan & Rai, Shesh N., 2009. "Assumption adequacy averaging as a concept for developing more robust methods for differential gene expression analysis," Computational Statistics & Data Analysis, Elsevier, vol. 53(5), pages 1604-1612, March.
    • Handle: RePEc:eee:csdana:v:53:y:2009:i:5:p:1604-1612
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    1. Allison, David B. & Gadbury, Gary L. & Heo, Moonseong & Fernandez, Jose R. & Lee, Cheol-Koo & Prolla, Tomas A. & Weindruch, Richard, 2002. "A mixture model approach for the analysis of microarray gene expression data," Computational Statistics & Data Analysis, Elsevier, vol. 39(1), pages 1-20, March.
    2. David J. Spiegelhalter & Nicola G. Best & Bradley P. Carlin & Angelika Van Der Linde, 2002. "Bayesian measures of model complexity and fit," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 64(4), pages 583-639, October.
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    1. Pounds Stanley B. & Gao Cuilan L. & Zhang Hui, 2012. "Empirical Bayesian Selection of Hypothesis Testing Procedures for Analysis of Sequence Count Expression Data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(5), pages 1-32, October.
    2. Demba Fofana & E. O. George & Dale Bowman, 2021. "Combining assumptions and graphical network into gene expression data analysis," Journal of Statistical Distributions and Applications, Springer, vol. 8(1), pages 1-17, December.
    3. Park, DoHwan & Park, Junyong & Zhong, Xiaosong & Sadelain, Michel, 2011. "Estimation of empirical null using a mixture of normals and its use in local false discovery rate," Computational Statistics & Data Analysis, Elsevier, vol. 55(7), pages 2421-2432, July.

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