Normalization of Gene-Expression Microarray Data

Expression microarrays are designed to quantify the amount of mRNA in a specific sample. However, this can only be done indirectly through quantifying the color intensities returned by labeled mRNA molecules bound to the array surface. Translating pixel intensities into transcript expression requires a series of computations, generically known as preprocessing and normalization steps. In this chapter, we introduce the basic concepts and methods, and illustrate them using data from three commonly used commercial platforms.