基于确切检验的 RNA-seq 数据差异表达分析样本量计算。
Sample size calculation based on exact test for assessing differential expression analysis in RNA-seq data.
机构信息
Center for Quantitative Sciences, Vanderbilt University, 571 Preston Building Nashville, TN, USA.
出版信息
BMC Bioinformatics. 2013 Dec 6;14:357. 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.
背景
样本量计算是生物医学研究实验设计中的一个重要问题。对于 RNA-seq 实验，已经提出了基于泊松模型的样本量计算方法；然而，当存在生物学重复时，RNA-seq 数据可能表现出比平均值大得多的变异（即过度离散）。泊松模型不能适当地对过度离散进行建模，在这种情况下，负二项式模型已被用作泊松模型的自然扩展。由于目前缺乏基于负二项式模型的用于评估 RNA-seq 数据差异表达分析的样本量计算方法，我们提出了一种计算样本量的方法。
结果
我们提出了一种基于确切检验的方法来计算用于评估 RNA-seq 数据差异表达分析的样本量。
结论
所提出的样本量计算方法简单直接，计算量不大。提出了评估所提出的样本量方法性能的模拟研究；结果表明，我们的方法效果良好，达到了预期的功效。
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