Design of studies using DNA microarrays

DNA microarrays are assays that simultaneously provide information about expression levels of thousands of genes and are consequently finding wide use in biomedical research. In order to control the many sources of variation and the many opportunities for misanalysis, DNA microarray studies require careful planning. Different studies have different objectives, and important aspects of design and analysis strategy differ for different types of studies. We review several types of objectives of studies using DNA microarrays and address issues such as selection of samples, levels of replication needed, allocation of samples to dyes and arrays, sample size considerations, and analysis strategies.