Microarrays are routinely used to assess mRNA transcript levels on a genome-wide scale. As use and acceptance increases, there is intensified focus on appropriate methods of data generation and interpretation, with important questions being asked about the best data analysis methods. The development of such 'best practices' is needed, as microarrays — in particular, Affymetrix oligonucleotide arrays — are becoming increasingly important in human clinical trials, both for differential diagnosis and monitoring of pharmacological efficacy. Here, representatives from high-volume microarray core centres consider the current status of 'best practices', focusing on the broadly used Affymetrix oligonucleotide arrays.