Design and Analysis of Screening Experiments with Microarrays

Microarrays are an important exploratory tool in many screening experiments. There are multiple objectives for these experiments including the identification of genes that change expression under two or more biological conditions, the discovery of new cellular or molecular functions of genes, and the definition of a molecular profile that characterizes different biological conditions underlying, for example, normal or tumor cells. The technology of microarrays is first described, followed by some simple comparative experiments and some of the statistical techniques that are used for their analysis. A very important question arising in the design of screening experiments with microarrays is the choice of the sample size and we describe two approaches to sample size determination. The first approach is based on the concept of reproducibility, and the second uses a Bayesian decisiontheoretic criterion to make a trade-off between information gain and experiment costs. Finally some of the open problems in the design and analysis of microarray experiments are discussed.