Questions and Answers on Design of Dual-Label Microarrays for Identifying Differentially Expressed Genes

The rapid growth in the use of microarrays has generated many questions about how to design experiments that use this technology effectively. Investigators need answers to questions about RNA sample selection, allocation of samples to arrays, robustness of design, dye bias, sample size, and statistical power to ensure that the experimental objectives are achieved. We address some common questions that arise in designing duallabel microarray experiments and provide statistical answers to these questions, focusing specifically on how to select optimal designs for the identification of differentially expressed genes.