Abstract: In the last years, biostatistical research has begun to apply linear
models and design theory to develop efficient experimental designs and analysis
tools for gene expression microarray data. With two-colour microarrays, direct
comparisons of RNA-targets are possible and lead to incomplete block designs.
In this setting, efficient designs for simple and factorial microarray
experiments have mainly been proposed for technical replicates. But for
biological replicates, which are crucial to obtain inference that can be
generalised to a biological population, this question has only been discussed
recently and is not fully solved yet. In this paper, we propose efficient
designs for independent two-sample experiments using two-colour microarrays
enabling biologists to measure their biological random samples in an efficient
manner to draw generalisable conclusions. We give advice for experimental
situations with differing group sizes and show the impact of different designs
on the variance and degrees of freedom of the test statistics. The designs
proposed in this paper can be evaluated using SAS PROC MIXED or
S+/R lme.
Keywords: microarray, design, biological replication, mixed linear model, ANOVA
