A-Optimal Designs for Two-Color Microarray Experiments for Treatment-Control and All-to-Next Contrasts

Two-color microarray experiments form an important tool in gene expression analysis. Due to the high costs of microarray experiments it is fundamental to plan these experiments carefully. Therefore, we propose a method to construct A-optimal block designs which can be adapted to construct nearly optimal microarray experiments. This method can be applied to derive A-optimal designs for arbitrary contrast settings. In this article, we focus on treatment control comparisons and all-to-next contrasts. We will show that our designs are more efficient than the designs currently in practice.