Sample size calculation based on exact test for assessing differential expression analysis in RNA-seq data
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
BMC Bioinformatics 2013, 14:357 doi:10.1186/1471-2105-14-357Published: 6 December 2013
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.
We propose a sample size calculation method based on the exact test for assessing differential expression analysis of RNA-seq data.
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.