Volume 14 Supplement 17

Proceedings of the 12th Annual UT-ORNL-KBRIN Bioinformatics Summit 2013

Open Access

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

BMC Bioinformatics201314(Suppl 17):A21


Published: 22 October 2013


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.


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.

Authors’ Affiliations

Department of Biostatistics, St. Jude Children’s Research Hospital
Department of Mathematics, University of Tennessee Chattanooga


© Pounds and Gao; licensee BioMed Central Ltd. 2013

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.