Designing, Performing, and Interpreting a Microarray-Based Gene Expression Study

Microarray-based assays have significantly expanded their scope and range of applications over the last 10 years, and – at least for gene expression – can be considered mainstream applications. High-throughput, microarray-based gene expression studies have proven particularly useful in the study of neurodegenerative diseases, for which they have provided key insights in understanding disease pathogenesis, regional and cellular specificity, and identification of therapeutic targets. Even though many experimental steps are currently performed in specialized core facilities, the key steps of a microarray study – experimental design, and data analysis and interpretation – are performed by the primary investigator. Knowledge of the issues related to these key steps is essential to properly perform and interpret a microarray experiment and constitutes the main focus of the present chapter. The basic analytical steps are covered, and annotated R code for the analysis of a published dataset is provided.