, a bio/informatics shared resource is still "open for business" - Visit the CDS website


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

Li CI, Su PF, Shyr Y
BMC Bioinformatics. 2013 14: 357

PMID: 24314022 · PMCID: PMC3924199 · DOI:10.1186/1471-2105-14-357

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.

MeSH Terms (12)

Base Sequence Computer Simulation Gene Expression Regulation Likelihood Functions Models, Statistical Poisson Distribution Random Allocation Research Design RNA Sample Size Sequence Analysis, RNA User-Computer Interface

Connections (1)

This publication is referenced by other Labnodes entities:

Links