The Fundamentals of Constructing and Interpreting Heat Maps

: This chapter is intended to introduce the fundamental principles of the heat map, the most widely used medium to present high-throughput data, to scientists unaccustomed to analyzing large data sets. Its scope includes describing the general features of heat maps, how their components are designed, the meaning of parameters such as "distance method" and "linkage method," and the influence of manipulations such as row-scaling and logarithmic transformations on data interpretation and presentation. This chapter may serve as a guide to understanding the use of heat maps in published analyses or to aid in their design, allowing efficient interpretations of high-throughput experiments, exploration of hypotheses, or clear communications of findings.