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Empirical Bayesian selection of hypothesis testing procedures for analysis of digital gene expression data

Background

Differential expression analysis of digital gene expression data involves performing a large number of hypothesis tests that compare the expression count data of each gene or transcript across two or more biological conditions. The assumptions of any specific hypothesis-testing method will probably not be valid for each of a very large number of genes. Thus, computational evaluation of assumptions should be incorporated into the analysis to select an appropriate hypothesis-testing method for each gene.

Materials and methods

Here, we generalize earlier work to introduce two novel procedures that use estimates of the empirical Bayesian probability (EBP) of overdispersion to select or combine results of a standard Poisson likelihood ratio test and a quasi-likelihood test for each gene. These EBP-based procedures simultaneously evaluate the Poisson-distribution assumption and account for multiple testing. With adequate power to detect overdispersion, the new procedures select the standard likelihood test for each gene with Poisson-distributed counts and the quasi-likelihood test for each gene with overdispersed counts.

Results

The new procedures outperformed previously published methods in many simulation studies. We also present a real-data analysis example and discuss how the framework used to develop the new procedures may be generalized to further enhance performance.

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Correspondence to Cuilan Gao.

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This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Pounds, S., Gao, C. Empirical Bayesian selection of hypothesis testing procedures for analysis of digital gene expression data. BMC Bioinformatics 14, A21 (2013). https://doi.org/10.1186/1471-2105-14-S17-A21

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Keywords

  • Likelihood Ratio
  • Multiple Testing
  • Likelihood Ratio Test
  • Ratio Test
  • Count Data