This paper describes the theoretical and practical issues in experimental design for gene expression microarrays. Specifically, this paper (1) discusses the basic principles of design (randomization, replication, and blocking) as they pertain to microarrays, and (2) provides some general guidelines for statisticians designing microarray studies.
Design of Experiments and Sample Surveys | Microarrays
Kerr, M. Kathleen, "Design Considerations for Efficient and Effective Microarray Studies" (June 2003). UW Biostatistics Working Paper Series. Working Paper 210.