Microarray technology is a powerful tool for animal functional genomics studies, with applications spanning from gene identification and mapping, to function and control of gene expression. Microarray assays, however, are complex and costly, and hence generally performed with relatively small number of animals. Nevertheless, they generate data sets of unprecedented complexity and dimensionality. Therefore, such trials require careful planning and experimental design, in addition to tailored statistical and computational tools for their appropriate data mining. In this review, we discuss experimental design and data analysis strategies, which incorporate prior genomic and biological knowledge, such as genotypes and gene function and pathway membership. We focus the discussion on the design of genetical genomics studies, and on significance testing for detection of differential expression. It is shown that the use of prior biological information can improve the efficiency of microarray experiments.
