Statistical designs for two-color microarray experiments involving technical replication

In a two-color microarray experiment, we consider the issues of determination of which mRNA samples are to be labeled with which fluorescent dye and which mRNA samples are to be hybridized together on the same slide. Specific attention is given to the test–control experiments whose primary interest lies in comparing several test treatments with a control treatment. A statistical linear model is proposed to characterize two major sources of systematic variation: the variation among distinct slides and that between fluorescent dyes. Furthermore, the possible correlation due to technical replication is also incorporated into the model. A series of A-optimal or highly efficient designs are generated from a heuristic algorithm based on the proposed model. It is shown that the obtained designs are robust not only to the variation of the correlation because of technique replication, but also to the loss of one or two slides. In addition, the comparative experiments involving technical replication are also discussed.