Optimizing experiment and analysis parameters for spotted microarrays

This chapter outlines considerations and methods of experimental design for spotted microarray studies that contribute to the robustness of the acquired data. The chapter is divided into two principal sections: (1) a summary of factors that affect the quality of individual array results; and (2) a discussion of experimental design features and replication criteria that enable researchers to gain confidence in their findings. The goal of section (2) is to promote the careful design of microarray studies, with downstream statistical analysis in mind, such that a minimal amount of biological and/or technical replication is required to achieve reproducible results. Topics addressed include choosing appropriate samples to be compared, determining the optimal amount of sample to use, flagging uninformative data, establishing confidence limits in normalized data and the application of statistical tests to identify differentially expressed genes.