Download or read book Modelling and Resampling Based Multiple Testing with Applications to Genetics written by Yifan Huang and published by . This book was released on 2005 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract: Multiple hypotheses testing is a common problem in practice. For instance, in microarray experiments, whether the goal is to select maintenance genes for normalization or to identify differentially expressed genes between samples, multiple genes are under consideration. Multiplicity inflates the type I error rate of the hypothesis testing, so we need to adjust the testing procedure to control the overly error rate. My research focuses on the strong control of Familywise Error Rate (FWER). There are mainly two different types of approaches to multiple testing. One is modelling based approach and the other non-modelling based. Modelling based approaches fit models to the data so that the joint distribution of the test statistics is tractable. Non-modelling based approaches consist of inequality based methods and resampling based methods. They require less or no information about the joint distribution of the test statistics. I have shown in Chapter 1 that frequently used Hochberg's step-up method is a special case of partition testing based on Simes' test. This is a new result. Hochberg's step-up method is an inequity based non-modelling partition testing. Modelling based partition testing is applicable whether the joint distribution of the test statistics is known or not. By applying modelling based partition testing when the joint distribution of test statistics is known, I illustrate that modelling based approaches are often more powerful than inequality based non-modelling approaches. In Chapter 2, I construct counterexamples to the validity of permutation test, demonstrating that the resampling based methods are often invalid. My results suggest recommendation of modelling based approaches. When the joint distribution of the test statistics is untractable, modelling followed by bootstrap can be applied. I use modelling followed by bootstrap in Chapter 3 to select maintenance genes for normalizing the gene expression data.

Download or read book Multiple Testing Procedures with Applications to Genomics written by Sandrine Dudoit and published by Springer Science & Business Media. This book was released on 2007-12-18 with total page 611 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book establishes the theoretical foundations of a general methodology for multiple hypothesis testing and discusses its software implementation in R and SAS. These are applied to a range of problems in biomedical and genomic research, including identification of differentially expressed and co-expressed genes in high-throughput gene expression experiments; tests of association between gene expression measures and biological annotation metadata; sequence analysis; and genetic mapping of complex traits using single nucleotide polymorphisms. The procedures are based on a test statistics joint null distribution and provide Type I error control in testing problems involving general data generating distributions, null hypotheses, and test statistics.

Download or read book Multiple Testing Procedures with Applications to Genomics written by Sandrine Dudoit and published by Springer. This book was released on 2008-11-01 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book establishes the theoretical foundations of a general methodology for multiple hypothesis testing and discusses its software implementation in R and SAS. These are applied to a range of problems in biomedical and genomic research, including identification of differentially expressed and co-expressed genes in high-throughput gene expression experiments; tests of association between gene expression measures and biological annotation metadata; sequence analysis; and genetic mapping of complex traits using single nucleotide polymorphisms. The procedures are based on a test statistics joint null distribution and provide Type I error control in testing problems involving general data generating distributions, null hypotheses, and test statistics.

Download or read book Resampling Based Multiple Testing written by Peter H. Westfall and published by John Wiley & Sons. This book was released on 1993-01-12 with total page 382 pages. Available in PDF, EPUB and Kindle. Book excerpt: Combines recent developments in resampling technology (including the bootstrap) with new methods for multiple testing that are easy to use, convenient to report and widely applicable. Software from SAS Institute is available to execute many of the methods and programming is straightforward for other applications. Explains how to summarize results using adjusted p-values which do not necessitate cumbersome table look-ups. Demonstrates how to incorporate logical constraints among hypotheses, further improving power.

Download or read book Statistical Modeling for Biological Systems written by Anthony Almudevar and published by Springer Nature. This book was released on 2020-03-11 with total page 361 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book commemorates the scientific contributions of distinguished statistician, Andrei Yakovlev. It reflects upon Dr. Yakovlev’s many research interests including stochastic modeling and the analysis of micro-array data, and throughout the book it emphasizes applications of the theory in biology, medicine and public health. The contributions to this volume are divided into two parts. Part A consists of original research articles, which can be roughly grouped into four thematic areas: (i) branching processes, especially as models for cell kinetics, (ii) multiple testing issues as they arise in the analysis of biologic data, (iii) applications of mathematical models and of new inferential techniques in epidemiology, and (iv) contributions to statistical methodology, with an emphasis on the modeling and analysis of survival time data. Part B consists of methodological research reported as a short communication, ending with some personal reflections on research fields associated with Andrei and on his approach to science. The Appendix contains an abbreviated vitae and a list of Andrei’s publications, complete as far as we know. The contributions in this book are written by Dr. Yakovlev’s collaborators and notable statisticians including former presidents of the Institute of Mathematical Statistics and of the Statistics Section of the AAAS. Dr. Yakovlev’s research appeared in four books and almost 200 scientific papers, in mathematics, statistics, biomathematics and biology journals. Ultimately this book offers a tribute to Dr. Yakovlev’s work and recognizes the legacy of his contributions in the biostatistics community.

Download or read book Simultaneous Statistical Inference written by Thorsten Dickhaus and published by Springer Science & Business Media. This book was released on 2014-01-23 with total page 182 pages. Available in PDF, EPUB and Kindle. Book excerpt: This monograph will provide an in-depth mathematical treatment of modern multiple test procedures controlling the false discovery rate (FDR) and related error measures, particularly addressing applications to fields such as genetics, proteomics, neuroscience and general biology. The book will also include a detailed description how to implement these methods in practice. Moreover new developments focusing on non-standard assumptions are also included, especially multiple tests for discrete data. The book primarily addresses researchers and practitioners but will also be beneficial for graduate students.

Download or read book Modeling Dose Response Microarray Data in Early Drug Development Experiments Using R written by Dan Lin and published by Springer Science & Business Media. This book was released on 2012-08-27 with total page 285 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book focuses on the analysis of dose-response microarray data in pharmaceutical settings, the goal being to cover this important topic for early drug development experiments and to provide user-friendly R packages that can be used to analyze this data. It is intended for biostatisticians and bioinformaticians in the pharmaceutical industry, biologists, and biostatistics/bioinformatics graduate students. Part I of the book is an introduction, in which we discuss the dose-response setting and the problem of estimating normal means under order restrictions. In particular, we discuss the pooled-adjacent-violator (PAV) algorithm and isotonic regression, as well as inference under order restrictions and non-linear parametric models, which are used in the second part of the book. Part II is the core of the book, in which we focus on the analysis of dose-response microarray data. Methodological topics discussed include: • Multiplicity adjustment • Test statistics and procedures for the analysis of dose-response microarray data • Resampling-based inference and use of the SAM method for small-variance genes in the data • Identification and classification of dose-response curve shapes • Clustering of order-restricted (but not necessarily monotone) dose-response profiles • Gene set analysis to facilitate the interpretation of microarray results • Hierarchical Bayesian models and Bayesian variable selection • Non-linear models for dose-response microarray data • Multiple contrast tests • Multiple confidence intervals for selected parameters adjusted for the false coverage-statement rate All methodological issues in the book are illustrated using real-world examples of dose-response microarray datasets from early drug development experiments.

Download or read book Statistical Methods in Psychiatry and Related Fields written by Ralitza Gueorguieva and published by CRC Press. This book was released on 2017-11-20 with total page 371 pages. Available in PDF, EPUB and Kindle. Book excerpt: Data collected in psychiatry and related fields are complex because outcomes are rarely directly observed, there are multiple correlated repeated measures within individuals, there is natural heterogeneity in treatment responses and in other characteristics in the populations. Simple statistical methods do not work well with such data. More advanced statistical methods capture the data complexity better, but are difficult to apply appropriately and correctly by investigators who do not have advanced training in statistics. This book presents, at a non-technical level, several approaches for the analysis of correlated data: mixed models for continuous and categorical outcomes, nonparametric methods for repeated measures and growth mixture models for heterogeneous trajectories over time. Separate chapters are devoted to techniques for multiple comparison correction, analysis in the presence of missing data, adjustment for covariates, assessment of mediator and moderator effects, study design and sample size considerations. The focus is on the assumptions of each method, applicability and interpretation rather than on technical details. Features Provides an overview of intermediate to advanced statistical methods applied to psychiatry. Takes a non-technical approach with mathematical details kept to a minimum. Includes lots of detailed examples from published studies in psychiatry and related fields. Software programs, data sets and output are available on a supplementary website. The intended audience are applied researchers with minimal knowledge of statistics, although the book could also benefit collaborating statisticians. The book, together with the online materials, is a valuable resource aimed at promoting the use of appropriate statistical methods for the analysis of repeated measures data. Ralitza Gueorguieva is a Senior Research Scientist at the Department of Biostatistics, Yale School of Public Health. She has more than 20 years experience in statistical methodology development and collaborations with psychiatrists and other researchers, and is the author of over 130 peer-reviewed publications.

Download or read book Statistical Bioinformatics with R written by Sunil K. Mathur and published by Academic Press. This book was released on 2009-12-21 with total page 337 pages. Available in PDF, EPUB and Kindle. Book excerpt: Statistical Bioinformatics provides a balanced treatment of statistical theory in the context of bioinformatics applications. Designed for a one or two semester senior undergraduate or graduate bioinformatics course, the text takes a broad view of the subject – not just gene expression and sequence analysis, but a careful balance of statistical theory in the context of bioinformatics applications. The inclusion of R & SAS code as well as the development of advanced methodology such as Bayesian and Markov models provides students with the important foundation needed to conduct bioinformatics. Integrates biological, statistical and computational concepts Inclusion of R & SAS code Provides coverage of complex statistical methods in context with applications in bioinformatics Exercises and examples aid teaching and learning presented at the right level Bayesian methods and the modern multiple testing principles in one convenient book

Download or read book Big Data Analytics in Bioinformatics and Healthcare written by Wang, Baoying and published by IGI Global. This book was released on 2014-10-31 with total page 552 pages. Available in PDF, EPUB and Kindle. Book excerpt: As technology evolves and electronic data becomes more complex, digital medical record management and analysis becomes a challenge. In order to discover patterns and make relevant predictions based on large data sets, researchers and medical professionals must find new methods to analyze and extract relevant health information. Big Data Analytics in Bioinformatics and Healthcare merges the fields of biology, technology, and medicine in order to present a comprehensive study on the emerging information processing applications necessary in the field of electronic medical record management. Complete with interdisciplinary research resources, this publication is an essential reference source for researchers, practitioners, and students interested in the fields of biological computation, database management, and health information technology, with a special focus on the methodologies and tools to manage massive and complex electronic information.

Download or read book Encyclopedia of Artificial Intelligence written by Juan Ramon Rabunal and published by IGI Global. This book was released on 2009-01-01 with total page 1640 pages. Available in PDF, EPUB and Kindle. Book excerpt: "This book is a comprehensive and in-depth reference to the most recent developments in the field covering theoretical developments, techniques, technologies, among others"--Provided by publisher.

Download or read book Statistical Modeling and Analysis for Complex Data Problems written by Pierre Duchesne and published by Springer Science & Business Media. This book was released on 2005-12-05 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book reviews some of today’s more complex problems, and reflects some of the important research directions in the field. Twenty-nine authors – largely from Montreal’s GERAD Multi-University Research Center and who work in areas of theoretical statistics, applied statistics, probability theory, and stochastic processes – present survey chapters on various theoretical and applied problems of importance and interest to researchers and students across a number of academic domains.

Download or read book Multiple Hypothesis Testing written by Houston Nash Gilbert and published by . This book was released on 2009 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Statistical Analysis of Gene Expression Microarray Data written by Terry Speed and published by CRC Press. This book was released on 2003-03-26 with total page 237 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Download or read book DNA Microarrays and Related Genomics Techniques written by David B. Allison and published by CRC Press. This book was released on 2005-11-14 with total page 391 pages. Available in PDF, EPUB and Kindle. Book excerpt: Considered highly exotic tools as recently as the late 1990s, microarrays are now ubiquitous in biological research. Traditional statistical approaches to design and analysis were not developed to handle the high-dimensional, small sample problems posed by microarrays. In just a few short years the number of statistical papers providing approaches

Download or read book Biostatistical Genetics and Genetic Epidemiology written by Robert C. Elston and published by John Wiley & Sons. This book was released on 2002-04-22 with total page 860 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Human Genetics and Genetic Epidemiology" ist der 3. Band aus der sehr erfolgreichen Reihe 'Wiley Biostatistics Reference Series', die auf Artikeln der "Encyclopedia of Biostatistics" basiert. Dieser Band gibt einen topaktuellen und umfassenden Überblick über ein Forschungsgebiet, das insbesondere im Zuge des Human-Genomprojekts eine regelrechte Explosion an Forschungsaktivitäten erlebt hat. Enthalten sind komplett aktualisierte Artikel aus der "Encyclopedia of Biostatistics" sowie über 25% neue Artikel. Mit einem komplexen System an Querverweisen, die das Auffinden der gewünschten Information erheblich erleichtern. Eine interessante Lektüre für Genetiker, Epidemiologen, Biostatistiker und Forscher in diesen Bereichen.

Download or read book Handbook of Statistics in Clinical Oncology written by John Crowley and published by CRC Press. This book was released on 2005-12-01 with total page 642 pages. Available in PDF, EPUB and Kindle. Book excerpt: A compendium of cutting-edge statistical approaches to solving problems in clinical oncology, Handbook of Statistics in Clinical Oncology, Second Edition focuses on clinical trials in phases I, II, and III, proteomic and genomic studies, complementary outcomes and exploratory methods. Cancer Forum called the first edition a