Sample size calculation through the incorporation of heteroscedasticity and dependence for a penalized t-statistic in microarray experiments

Abstract

When identifying the differentially expressed genes (DEGs) in microarray data, we often observe heteroscedasticity between groups and dependence among genes. Incorporating these factors is necessary for sample size calculation in microarray experiments. A penalized t-statistic is widely used to improve the identifiability of DEGs. We develop a formula to calculate sample size with dependence adjustment for the penalized t-statistic. Sample size is determined on the basis of overall power under certain conditions to maintain a certain false discovery rate. The usefulness of the proposed method is demonstrated by numerical studies using both simulated data and real data.