Gene expression microarray studies have led to interesting experimental designand statistical analysis challenges. The comparison of expression profiles acrosspopulations is one of the most common objectives of microarray experiments. Inthis manuscript we review some issues regarding design and statistical analysis fortwo-colour microarray platforms using mixed linear models, with special attentiondirected towards the different hierarchical levels of replication and the consequenteffect on the use of appropriate error terms for comparing experimental groups.We examine the traditional analysis of variance (ANOVA) models proposed formicroarray data and their extensions to hierarchically replicated experiments. Inaddition, we discuss a mixed model methodology for power and efficiency calculationsof different microarray experimental designs.
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