DNA microarrays are an important technology for studying gene expression. With a single hybridization, the level of expression of thousands of genes, or even an entire genome, can be estimated for a sample of cells. Consequently, many laboratories are attempting to utilize DNA micro arrays in their research. Whereaslaboratoriesarewellpreparedtoaddressthesignificantexperimental challenges in obtaining reproducible data from this RNA-based assay, inv- tigators are less prepared to analyze the large volumes of data produced by DNA microarrays. Although many software packages have been developed for the analysis of DNA microarray data, software alone is insufficient. One needs knowledge about the various aspects of data analysis in order to select and utilize software effectively. There is a plethora of analysis methods being published and it is difficult for biologists to determine which methods are valid and appropriate for their problems. Many scientists have learned that software is not an adequate substitute for biostatistical knowledge and seek statistical collaborators. Unfortunately, there is presently a shortage of statisticians who are available and knowled- able about DNA microarrays. For statisticians to be effective collaborators in anyarea,theymustinvestthetimetounderstandthesubjectmatterareaand become familiar with the literature so that they can ask the right questions and identify the key issues. Our objectives in this book are twofold: to provide scientists with infor- tion about the design and analysis of studies using DNA microarrays that will enable them to plan and analyze their own studies or to work with statistical collaborators effectively, and to aid statistical and computational scientists wishing to develop expertise in this area.