Analyzing Microarray Gene Expression Data


Book Description

A multi-discipline, hands-on guide to microarray analysis of biological processes Analyzing Microarray Gene Expression Data provides a comprehensive review of available methodologies for the analysis of data derived from the latest DNA microarray technologies. Designed for biostatisticians entering the field of microarray analysis as well as biologists seeking to more effectively analyze their own experimental data, the text features a unique interdisciplinary approach and a combined academic and practical perspective that offers readers the most complete and applied coverage of the subject matter to date. Following a basic overview of the biological and technical principles behind microarray experimentation, the text provides a look at some of the most effective tools and procedures for achieving optimum reliability and reproducibility of research results, including: An in-depth account of the detection of genes that are differentially expressed across a number of classes of tissues Extensive coverage of both cluster analysis and discriminant analysis of microarray data and the growing applications of both methodologies A model-based approach to cluster analysis, with emphasis on the use of the EMMIX-GENE procedure for the clustering of tissue samples The latest data cleaning and normalization procedures The uses of microarray expression data for providing important prognostic information on the outcome of disease




Bioinformatics and Computational Biology Solutions Using R and Bioconductor


Book Description

Full four-color book. Some of the editors created the Bioconductor project and Robert Gentleman is one of the two originators of R. All methods are illustrated with publicly available data, and a major section of the book is devoted to fully worked case studies. Code underlying all of the computations that are shown is made available on a companion website, and readers can reproduce every number, figure, and table on their own computers.




The Analysis of Gene Expression Data


Book Description

This book presents practical approaches for the analysis of data from gene expression micro-arrays. It describes the conceptual and methodological underpinning for a statistical tool and its implementation in software. The book includes coverage of various packages that are part of the Bioconductor project and several related R tools. The materials presented cover a range of software tools designed for varied audiences.




The EM Algorithm and Extensions


Book Description

The only single-source——now completely updated and revised——to offer a unified treatment of the theory, methodology, and applications of the EM algorithm Complete with updates that capture developments from the past decade, The EM Algorithm and Extensions, Second Edition successfully provides a basic understanding of the EM algorithm by describing its inception, implementation, and applicability in numerous statistical contexts. In conjunction with the fundamentals of the topic, the authors discuss convergence issues and computation of standard errors, and, in addition, unveil many parallels and connections between the EM algorithm and Markov chain Monte Carlo algorithms. Thorough discussions on the complexities and drawbacks that arise from the basic EM algorithm, such as slow convergence and lack of an in-built procedure to compute the covariance matrix of parameter estimates, are also presented. While the general philosophy of the First Edition has been maintained, this timely new edition has been updated, revised, and expanded to include: New chapters on Monte Carlo versions of the EM algorithm and generalizations of the EM algorithm New results on convergence, including convergence of the EM algorithm in constrained parameter spaces Expanded discussion of standard error computation methods, such as methods for categorical data and methods based on numerical differentiation Coverage of the interval EM, which locates all stationary points in a designated region of the parameter space Exploration of the EM algorithm's relationship with the Gibbs sampler and other Markov chain Monte Carlo methods Plentiful pedagogical elements—chapter introductions, lists of examples, author and subject indices, computer-drawn graphics, and a related Web site The EM Algorithm and Extensions, Second Edition serves as an excellent text for graduate-level statistics students and is also a comprehensive resource for theoreticians, practitioners, and researchers in the social and physical sciences who would like to extend their knowledge of the EM algorithm.




Statistical Analysis of Gene Expression Microarray Data


Book Description

Although less than a decade old, the field of microarray data analysis is now thriving and growing at a remarkable pace. Biologists, geneticists, and computer scientists as well as statisticians all need an accessible, systematic treatment of the techniques used for analyzing the vast amounts of data generated by large-scale gene expression studies




Mixture Models


Book Description

Mixture models are a powerful tool for analyzing complex and heterogeneous datasets across many scientific fields, from finance to genomics. Mixture Models: Parametric, Semiparametric, and New Directions provides an up-to-date introduction to these models, their recent developments, and their implementation using R. It fills a gap in the literature by covering not only the basics of finite mixture models, but also recent developments such as semiparametric extensions, robust modeling, label switching, and high-dimensional modeling. Features Comprehensive overview of the methods and applications of mixture models Key topics include hypothesis testing, model selection, estimation methods, and Bayesian approaches Recent developments, such as semiparametric extensions, robust modeling, label switching, and high-dimensional modeling Examples and case studies from such fields as astronomy, biology, genomics, economics, finance, medicine, engineering, and sociology Integrated R code for many of the models, with code and data available in the R Package MixSemiRob Mixture Models: Parametric, Semiparametric, and New Directions is a valuable resource for researchers and postgraduate students from statistics, biostatistics, and other fields. It could be used as a textbook for a course on model-based clustering methods, and as a supplementary text for courses on data mining, semiparametric modeling, and high-dimensional data analysis.




Finite Mixture Models


Book Description

An up-to-date, comprehensive account of major issues in finitemixture modeling This volume provides an up-to-date account of the theory andapplications of modeling via finite mixture distributions. With anemphasis on the applications of mixture models in both mainstreamanalysis and other areas such as unsupervised pattern recognition,speech recognition, and medical imaging, the book describes theformulations of the finite mixture approach, details itsmethodology, discusses aspects of its implementation, andillustrates its application in many common statisticalcontexts. Major issues discussed in this book include identifiabilityproblems, actual fitting of finite mixtures through use of the EMalgorithm, properties of the maximum likelihood estimators soobtained, assessment of the number of components to be used in themixture, and the applicability of asymptotic theory in providing abasis for the solutions to some of these problems. The author alsoconsiders how the EM algorithm can be scaled to handle the fittingof mixture models to very large databases, as in data miningapplications. This comprehensive, practical guide: * Provides more than 800 references-40% published since 1995 * Includes an appendix listing available mixture software * Links statistical literature with machine learning and patternrecognition literature * Contains more than 100 helpful graphs, charts, and tables Finite Mixture Models is an important resource for both applied andtheoretical statisticians as well as for researchers in the manyareas in which finite mixture models can be used to analyze data.




Analysis of Microarray Gene Expression Data


Book Description

After genomic sequencing, microarray technology has emerged as a widely used platform for genomic studies in the life sciences. Microarray technology provides a systematic way to survey DNA and RNA variation. With the abundance of data produced from microarray studies, however, the ultimate impact of the studies on biology will depend heavily on data mining and statistical analysis. The contribution of this book is to provide readers with an integrated presentation of various topics on analyzing microarray data.




A Practical Approach to Microarray Data Analysis


Book Description

In the past several years, DNA microarray technology has attracted tremendous interest in both the scientific community and in industry. With its ability to simultaneously measure the activity and interactions of thousands of genes, this modern technology promises unprecedented new insights into mechanisms of living systems. Currently, the primary applications of microarrays include gene discovery, disease diagnosis and prognosis, drug discovery (pharmacogenomics), and toxicological research (toxicogenomics). Typical scientific tasks addressed by microarray experiments include the identification of coexpressed genes, discovery of sample or gene groups with similar expression patterns, identification of genes whose expression patterns are highly differentiating with respect to a set of discerned biological entities (e.g., tumor types), and the study of gene activity patterns under various stress conditions (e.g., chemical treatment). More recently, the discovery, modeling, and simulation of regulatory gene networks, and the mapping of expression data to metabolic pathways and chromosome locations have been added to the list of scientific tasks that are being tackled by microarray technology. Each scientific task corresponds to one or more so-called data analysis tasks. Different types of scientific questions require different sets of data analytical techniques. Broadly speaking, there are two classes of elementary data analysis tasks, predictive modeling and pattern-detection. Predictive modeling tasks are concerned with learning a classification or estimation function, whereas pattern-detection methods screen the available data for interesting, previously unknown regularities or relationships.