Adjusted Sample Size Calculation for RNA-seq Data in the Presence of Confounding Covariates

Abstract

Sample size calculation for adequate power analysis is critical in optimizing RNA-seq experimental design. However, the complexity increases for directly estimating sample size when taking into consideration confounding covariates. Although a number of approaches for sample size calculation have been proposed for RNA-seq data, most ignore any potential heterogeneity. In this study, we implemented a simulation-based and confounder-adjusted method to provide sample size recommendations for RNA-seq differential expression analysis. The data was generated using Monte Carlo simulation, given an underlined distribution of confounding covariates and parameters for a negative binomial distribution. The relationship between the sample size with the power and parameters, such as dispersion, fold change and mean read counts, can be visualized. We demonstrate that the adjusted sample size for a desired power and type one error rate of α is usually larger when taking confounding covariates into account. More importantly, our simulation study reveals that sample size may be underestimated by existing methods if a confounding covariate exists in RNA-seq data. Consequently, this underestimate could affect the detection power for the differential expression analysis. Therefore, we introduce confounding covariates for sample size estimation for heterogeneous RNA-seq data.