<p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p> <p>Gene expression microarray studies have led to interesting experimental design
and statistical analysis challenges. The comparison of expression profiles across
populations is one of the most common objectives of microarray experiments. In
this manuscript we review some issues regarding design and statistical analysis for
two-colour microarray platforms using mixed linear models, with special attention
directed towards the different hierarchical levels of replication and the consequent
effect on the use of appropriate error terms for comparing experimental groups.
We examine the traditional analysis of variance (ANOVA) models proposed for
microarray data and their extensions to hierarchically replicated experiments. In
addition, we discuss a mixed model methodology for power and efficiency calculations
of different microarray experimental designs.</p>
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Comp Funct Genomics. 2005 Apr; 6(3):123-131