On reference designs for microarray experiments

We compare four variants of the reference design for microarray experiments in terms of their relative efficiency. A common reference sample across arrays is the most extensively used variation in practice, but independent samples from a reference group have also been considered in previous works. The relative efficiency of these designs depends of the number of treatments and the ratio between biological and technical variances. Here, we propose another alternative of reference structure, denoted by blocked reference design (BRD), in which each set (replication) of the treated samples is co-hybridized to an independent experimental unit of the control (reference) group. We provide efficiency curves for each pair of designs under different scenarios of variance ratio and number of treatments groups. The results show that the BRD is more efficient and less expensive than the traditional reference designs. Among the situations where the BRD is likely to be preferable we list time course experiments with a baseline and drug experiments with a placebo group.