An Introduction to DNA Microarrays

Oligonucleotide and DNA arrays, or microarrays, have proven to be useful tools to investigate biological function, and are the focal point of an increasing number of studies. However, most papers shed little light on the underlying basis and best use of microarray technology, often leaving a number of important questions unanswered. Under what conditions are microarrays helpful? How should microarray data be analyzed? What data analysis methods should be avoided? Which biological questions can microarrays address? Which biological questions are not best answered by microarrays? Here, we examine the technology itself, the data produced, proper experimental design, data analysis techniques, and experimental validation. These are issues important to all users of DNA arrays, from the mathematician who may have only limited knowledge of the biology behind the technology, to the biologist who is concerned with experimental design and the details of data analysis. Finally, we stress the importance of great experimental care, sample and data triage, well-characterized and rigorous analysis, and the need for appropriate follow-up and verification, especially when using animal or human tissue.

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