2 Methodology of microarray data analysis

A variety of data analysis tools has been developed to accommodate the various applications for microarray analysis. This chapter discusses some common analytical strategies for expression analysis, which can be potentially adapted for most microarray applications. The major steps involved in microarray data analysis are (1) microarray image acquisition and raw data generation, (2) data normalization and transformation, (3) classification and exploratory data analysis, and (4) post-analysis follow-up and validation. The first step, microarray image acquisition and raw data generation, is heavily platform dependent. Regardless of the approach chosen, the arrays are scanned after hybridization. Independent grayscale images, typically 16 bit tagged information file format files (tiff), are generated for each sample to be analyzed. Image analysis software is then used to identify arrayed spots and measure the relative fluorescence intensities for each element. There are many commercial and freely available software packages for image quantitation. Although there are differences between various imaging software, most give high quality, reproducible measures of hybridization intensities.

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