Cost-efficiency considerations in the choice of a microarray platform for time course experimental designs

Customarily, the choice between one- or two-colour microarray platforms is based on their respective practical and technical merits, contingent on objectives and constraints of the study at stake. Statistical efficiency, if accounted for, plays a secondary role. A cost-efficiency comparison of the one- and two-colour designs for a 2x4 time course experiment was conducted. It is shown that differences in costs between the platforms' designs, once adjusted for statistical efficiency, are not always negligible. The extent of these differences is largely influenced by subjects and array prices as well as by biological and error variances in their relative magnitude. Circumstances are described, in which cost-efficiency considerations will have an added value in motivating the selection of a microarray platform at the design stage.