Use of external controls in microarray experiments

DNA microarray analysis has become the most widely used technique for the study of gene expression patterns on a genomic scale. Microarray analysis is a complex technique involving many steps, and a number of commercial and in-house developed arrays and protocols for data collection and analysis are used in different laboratories. Inclusion of external or spike-in RNA controls allows one to evaluate the variability in gene expression measurements and to facilitate the comparison of data collected using different platforms and protocols. This chapter describes what external controls are, which collections of spike-in controls are available to researchers, and how they are implemented in the laboratory. Applications of external controls in the assessment of microarray performance, normalization strategies, the evaluation of algorithms for gene expression analysis, and the potential to quantify absolute mRNA levels are discussed.