An introduction to microarray data analysis and visualization

Microarray experiments offer a potential wealth of information but also present a significant data analysis challenge. A typical microarray data analysis project involves many interconnected manipulations of the raw experimental values, and each stage of the analysis challenges the experimenter to make decisions regarding the proper selection and usage of a variety of statistical techniques. In this chapter, we will provide an overview of each of the major stages of a typical yeast microarray project. We will focus on providing a solid conceptual foundation to help the reader better understand each of these steps, will highlight useful software tools, and will suggest best practices where applicable.