Gene expression analysis has progressed rapidly over the past decade from the historical analyses of individual genes to the sophisticated genome surveys routinely performed today. DNA biochips have facilitated this progression and helped accelerate target validation and drug discovery efforts by the pharmaceutical industry. The increasing use and acceptance of biochips to study genetic and cellular processes is clearly demonstrated by the large number of publications in recent years and the emergence of several robust commercial microarray platforms (1-3). Affymetrix (Santa Clara, Ca) pioneered this field and has been the market leader for many years, applying photolithographic technologies derived from the semiconductor industry to the fabrication of high-density 25-mer oligonucleotide microarrays. Alternative commercial platforms equally as robust have emerged including array platforms from Agilent, Amersham, Illumina and Applied Biosystems (see Chapter 1 of this book for further discussion of the technology platforms).