Introduction

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.

Publications

  1. Sample size calculation based on exact test for assessing differential expression analysis in RNA-seq data.
    Cite this
    Li CI, Su PF, Shyr Y, 2013-12-01 - BMC bioinformatics

Credits

  1. Chung-I Li
    Developer

  2. Pei-Fang Su
    Developer

  3. Yu Shyr
    Investigator

    Center for Quantitative Sciences, Vanderbilt University, United States of America

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Summary
AccessionBT006925
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByYu Shyr