DNA Microarray Data Analysis

A DNA microarray consists of a solid surface – which can be a glass slide, a nylon filter, or a quartz wafer – on which single strands of complementary DNA (cDNA) are immobilized on spots at fixed locations in a regular, often rectangular pattern (Figure 1). The number of spotted cDNA probes on a single array varies between a few hundred to over 30,000. Each spot is related to a single gene, although multiple spots can represent the same gene. From a sample of interest, the mRNA is then extracted, reverse transcribed to cDNA, labeled, and washed over the array. The target cDNA binds to those probes that have complementary base sequences, in a process known as hybridization. Measuring the labeling intensity of each spot then gives a value that should be proportional to the abundance of the corresponding mRNA transcript in the sample.

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