Abstract
Microarrays provide a valuable tool for the quantification of gene expression. Usually, however, there is a limited number of replicates leading to unsatisfying variance estimates in a geneโwise mixed model analysis. As thousands of genes are available, it is desirable to combine information across genes. When more than two tissue types or treatments are to be compared it might be advisable to consider the array effect as random. Then information between arrays may be recovered, which can increase accuracy in estimation. We propose a method of variance component estimation across genes for a linear mixed model with two random effects. The method may be extended to models with more than two random effects. We assume that the variance components follow a logโnormal distribution. Assuming that the sums of squares from the geneโwise analysis, given the true variance components, follow a scaled ฯ^2^โdistribution, we adopt an empirical Bayes approach. The variance components are estimated by the expectation of their posterior distribution. The new method is evaluated in a simulation study. Differentially expressed genes are more likely to be detected by tests based on these variance estimates than by tests based on geneโwise variance estimates. This effect is most visible in studies with small array numbers. Analyzing a real data set on maize endosperm the method is shown to work well. (ยฉ 2008 WILEYโVCH Verlag GmbH & Co. KGaA, Weinheim)