The Analysis of Gene Expression Data : Methods and Software Thedevelopmentoftechnologiesforhigh–throughputmeasurementofgene expression in biological system is providing powerful new tools for inv tigating the transcriptome on a genomic scale and across diverse biol ical systems and experimental designs. This technological transformation is generating an increasing demand for data analysis in biological inv tigations of gene expression. This book focuses on data analysis of gene expression microarrays. The goal is to provide guidance to practitioners in deciding which statistical approaches and packages may be indicated for their projects in choosing among the various options provided by those packages and in correctly interpreting the results. The book is a collection of chapters written by authors of statistical so ware for microarray data analysis. Each chapter describes the conceptual and methodological underpinning of data analysis tools as well as their software implementation and will enable readers to both understand and implement an analysis approach. Methods touch on all aspects of statis cal analysis of microarrays from annotation and ltering to clustering and classication. All software packages described are free to academic users. The materials presented cover a range of software tools designed for varied audiences. Some chapters describe simple menu driven software in a user friendly fashion and are designed to be accessible to microarray data analystswithoutformalquantitativetraining.Mostchaptersaredirectedat microarray data analysts with master’s level training in computer science biostatistics or bioinformatics. A minority of more advanced chapters are intended for doctoral students and researchers. The Analysis of Gene Expression Data: An Overview of Methods and Software Visualization and Annotation of Genomic Experiments Bioconductor R Packages for Exploratory Analysis and Normalization of cDNA Microarray Data An R Package for Analyses of Affymetrix Oligonucleotide Arrays DNA Chip Analyzer (dChip) Expression Profiler An S PLUS Library for the Analysis and Visualization of Differential Expression Dragon and Dragon View: Methods for the Annotation Analysis and Visualization of Large Scale Gene Expression Data Snomad: Biologist Friendly Web Tools for the Standardization and NOrmalization of Microarray Data Microarray Analysis Using the MicroArray Explorer Parametric Empirical Bayes Methods for Microarrays SAM Thresholding and False Discovery Rates for Detecting Differential Gene Expression in DNA Microarrays Adaptive Gene Picking with Microarray Data: Detecting Important Low Abundance Signals MAANOVA: A Software Package for the Analysis of Spotted cDNA Microarray Experiments GeneClust POE: Statistical Methods for Qualitative Analysis of Gene Expression Bayesian Decomposition Bayesian Clustering of Gene Expression Dynamics Relevance Networks: A First Step Toward Finding Genetic Regulatory Networks Within Microarray Data.