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This chapter discusses the design and analysis of relatively simple comparative experiments involving microarrays. Some of the discussion applies to all the most widely used kinds of microarrays, that is, radiolabelled cDNA arrays on nylon membranes, two-color, fluorescently labeled cDNA or long oligonucleotide arrays on glass slides, or single color, fluorescently labeled, high-density short oligonucleotide arrays on silicon chips. The main focus, however, is on two-color complementary deoxyribonucleic acid (cDNA) or long oligonucleotide arrays on glass slides because they present more challenging design and analysis problems than the other two kinds.
Terence P. Speed (Wed,) studied this question.