Since their conception in the mid–1990s, the use of microarrays has spread rapidly throughout the research community. So much so that, in recent years, a microarray experiment has become the ‘must–have’ item for many primary research articles. This trend is certainly not going out of fashion, as the range of applications for microarrays continues to grow and expand. This is why our second Nature Reviews collection features microarrays.

Researchers who carry out microarray experiments ask big questions, and the results generate large quantities of data. Analytical power has therefore had to step up to the challenges that have been created by microarray technology. In the first review in our collection, Atul Butte discusses the different ways in which large sets of microarray data can be analysed and then considers the remaining challenges in interpreting these results. Another problem arises from analysing genome–wide data sets that were generated using different approaches. Björn Grünenfelder and Elizabeth A. Winzeler discuss these issues, using yeast as a case study.

So what of other applications for microarrays? They are being used to understand disease pathogenesis, which might facilitate the identification of drug targets, as discussed by Lawrence Steinman and Scott Zamvil for multiple sclerosis. The perspective by David J. Lockhart and Carrolee Barlow further demonstrates how microarrays can be used for a fact–finding mission, to address old questions and generate new hypotheses about brain function and disease. As with all Nature Reviews journals, we also have a highlights section. These discuss microarray–related primary research articles that were published in 2003 and 2004, and provide information on yet more of the current issues, discoveries and applications.

In an accompanying web focus, we provide links to more microarray articles — highlights, reviews, research, and news and views — from across the Nature Publishing Group. This includes a March 2004 Nature Reviews Genetics article from The Tumour Analysis Best Practices Working Group, which proposes guidelines to aid in the generation and analysis of microarray data in clinical trials. All content can be found at www.nature.com/reviews/focus/microarrays.

Finally, we would like to thank Affymetrix for their financial support, which has allowed us to produce this collection and to make the featured articles free online for 6 months. The editorial content is, of course, the sole responsibility of the Nature Publishing Group.