Microarrays are useful tools to investigate the expression of thousands of genes rapidly. Some researchers remain reluctant to use the technology, however, largely because of its expense. Careful design of a microarray experiment is key to generating cost-effective results. This article explores issues that researchers face when embarking on a microarray experiment for the first time. These include decisions about which microarray platform is available for the organism of interest, the degree of replication (biological and technical) needed and which design (direct or indirect, loop or balanced block) is suitable
