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Open Access Highly Accessed Methodology article

Sample size calculation based on exact test for assessing differential expression analysis in RNA-seq data

Chung-I Li13, Pei-Fang Su23 and Yu Shyr3*

Author Affiliations

1 Department of Applied Mathematics, National Chiayi University, Chiayi, Taiwan

2 Department of Statistics, National Cheng Kung University, Tainan, Taiwan

3 Center for Quantitative Sciences, Vanderbilt University, 571 Preston Building Nashville, TN, USA

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BMC Bioinformatics 2013, 14:357  doi:10.1186/1471-2105-14-357

Published: 6 December 2013

Abstract

Background

Sample size calculation is an important issue in the experimental design of biomedical research. For RNA-seq experiments, the sample size calculation method based on the Poisson model has been proposed; however, when there are biological replicates, RNA-seq data could exhibit variation significantly greater than the mean (i.e. over-dispersion). The Poisson model cannot appropriately model the over-dispersion, and in such cases, the negative binomial model has been used as a natural extension of the Poisson model. Because the field currently lacks a sample size calculation method based on the negative binomial model for assessing differential expression analysis of RNA-seq data, we propose a method to calculate the sample size.

Results

We propose a sample size calculation method based on the exact test for assessing differential expression analysis of RNA-seq data.

Conclusions

The proposed sample size calculation method is straightforward and not computationally intensive. Simulation studies to evaluate the performance of the proposed sample size method are presented; the results indicate our method works well, with achievement of desired power.