Pooling mRNA in microarray experiments and its effect on power

Abstract

Motivation: Microarrays can simultaneously measure the expression levels of many genes and are widely applied to study complex biological problems at the genetic level. To contain costs, instead of obtaining a microarray on each individual, mRNA from several subjects can be first pooled and then measured with a single array. mRNA pooling is also necessary when there is not enough mRNA from each subject. Several studies have investigated the impact of pooling mRNA on inferences about gene expression, but have typically modeled the process of pooling as if it occurred in some transformed scale. This assumption is unrealistic. Results: We propose modeling the gene expression levels in a pool as a weighted average of mRNA expression of all individuals in the pool on the original measurement scale, where the weights correspond to individual sample contributions to the pool. Based on these improved statistical models, we develop the appropriate F statistics to test for differentially expressed genes. We present formulae to calculate the power of various statistical tests under different strategies for pooling mRNA and compare resulting power estimates to those that would be obtained by following the approach proposed by Kendziorski et al. (2003). We find that the Kendziorski estimate tends to exceed true power and that the estimate we propose, while somewhat conservative, is less biased. We argue that it is possible to design a study that includes mRNA pooling at a significantly reduced cost but with little loss of information. © The Author 2007. Published by Oxford University Press. All rights reserved.