Author: Haiyan Xu Publisher: ISBN: Category : Bioinformatics Languages : en Pages :
Book Description
Abstract: In multiple testing, strong control of the familywise error rate (FWER) may be unnecessarily stringent in some situations such as bioinformatic studies. An alternative is to control the false discovery rate (FDR), the expected proportion of true null hypotheses among all rejected null hypotheses. However, in bioinformatic studies, the loss or cost of false discoveries often corresponds to the number rather than the proportion of false discoveries. Controlling the generalized familywise error rate (gFWER) controls the probability of incorrectly rejecting strictly more than m hypotheses. In this dissertation, we propose the generalized partitioning principle for constructing multiple tests that control gFWER. A set of sufficient conditions to shortcut generalized partitioning tests as step-down tests is provided. We show that, by being able to use information on the joint distribution of test statistics, step-down tests we propose can be more powerful than stepdown tests that ignore such information.
Author: Mark Chang Publisher: Springer Science & Business Media ISBN: 144199842X Category : Medical Languages : en Pages : 316
Book Description
Classic biostatistics, a branch of statistical science, has as its main focus the applications of statistics in public health, the life sciences, and the pharmaceutical industry. Modern biostatistics, beyond just a simple application of statistics, is a confluence of statistics and knowledge of multiple intertwined fields. The application demands, the advancements in computer technology, and the rapid growth of life science data (e.g., genomics data) have promoted the formation of modern biostatistics. There are at least three characteristics of modern biostatistics: (1) in-depth engagement in the application fields that require penetration of knowledge across several fields, (2) high-level complexity of data because they are longitudinal, incomplete, or latent because they are heterogeneous due to a mixture of data or experiment types, because of high-dimensionality, which may make meaningful reduction impossible, or because of extremely small or large size; and (3) dynamics, the speed of development in methodology and analyses, has to match the fast growth of data with a constantly changing face. This book is written for researchers, biostatisticians/statisticians, and scientists who are interested in quantitative analyses. The goal is to introduce modern methods in biostatistics and help researchers and students quickly grasp key concepts and methods. Many methods can solve the same problem and many problems can be solved by the same method, which becomes apparent when those topics are discussed in this single volume.
Author: Alex Dmitrienko Publisher: CRC Press ISBN: 1584889853 Category : Mathematics Languages : en Pages : 323
Book Description
Useful Statistical Approaches for Addressing Multiplicity IssuesIncludes practical examples from recent trials Bringing together leading statisticians, scientists, and clinicians from the pharmaceutical industry, academia, and regulatory agencies, Multiple Testing Problems in Pharmaceutical Statistics explores the rapidly growing area of multiple c
Author: Dan Lin Publisher: Springer Science & Business Media ISBN: 3642240070 Category : Mathematics Languages : en Pages : 285
Book Description
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.
Author: Sandrine Dudoit Publisher: Springer Science & Business Media ISBN: 0387493174 Category : Science Languages : en Pages : 611
Book Description
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.
Author: Ying Lu Publisher: World Scientific ISBN: 9814583324 Category : Medical Languages : en Pages : 1471
Book Description
The book aims to provide both comprehensive reviews of the classical methods and an introduction to new developments in medical statistics. The topics range from meta analysis, clinical trial design, causal inference, personalized medicine to machine learning and next generation sequence analysis. Since the publication of the first edition, there have been tremendous advances in biostatistics and bioinformatics. The new edition tries to cover as many important emerging areas and reflect as much progress as possible. Many distinguished scholars, who greatly advanced their research areas in statistical methodology as well as practical applications, also have revised several chapters with relevant updates and written new ones from scratch.The new edition has been divided into four sections, including, Statistical Methods in Medicine and Epidemiology, Statistical Methods in Clinical Trials, Statistical Genetics, and General Methods. To reflect the rise of modern statistical genetics as one of the most fertile research areas since the publication of the first edition, the brand new section on Statistical Genetics includes entirely new chapters reflecting the state of the art in the field.Although tightly related, all the book chapters are self-contained and can be read independently. The book chapters intend to provide a convenient launch pad for readers interested in learning a specific topic, applying the related statistical methods in their scientific research and seeking the newest references for in-depth research.
Author: Thorsten Dickhaus Publisher: Springer Science & Business Media ISBN: 3642451829 Category : Science Languages : en Pages : 182
Book Description
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.
Author: Frank Bretz Publisher: CRC Press ISBN: 1420010905 Category : Mathematics Languages : en Pages : 202
Book Description
Adopting a unifying theme based on maximum statistics, Multiple Comparisons Using R describes the common underlying theory of multiple comparison procedures through numerous examples. It also presents a detailed description of available software implementations in R. The R packages and source code for the analyses are available at http://CRAN.R-project.org After giving examples of multiplicity problems, the book covers general concepts and basic multiple comparisons procedures, including the Bonferroni method and Simes’ test. It then shows how to perform parametric multiple comparisons in standard linear models and general parametric models. It also introduces the multcomp package in R, which offers a convenient interface to perform multiple comparisons in a general context. Following this theoretical framework, the book explores applications involving the Dunnett test, Tukey’s all pairwise comparisons, and general multiple contrast tests for standard regression models, mixed-effects models, and parametric survival models. The last chapter reviews other multiple comparison procedures, such as resampling-based procedures, methods for group sequential or adaptive designs, and the combination of multiple comparison procedures with modeling techniques. Controlling multiplicity in experiments ensures better decision making and safeguards against false claims. A self-contained introduction to multiple comparison procedures, this book offers strategies for constructing the procedures and illustrates the framework for multiple hypotheses testing in general parametric models. It is suitable for readers with R experience but limited knowledge of multiple comparison procedures and vice versa. See Dr. Bretz discuss the book.
Author: Ranajit Chakraborty Publisher: Newnes ISBN: 0444518754 Category : Computers Languages : en Pages : 614
Book Description
The field of statistics not only affects all areas of scientific activity, but also many other matters such as public policy. A series of handbooks is the only way of presenting the various aspects of statistical methodology, applications and developments. This volume deals with bioinformatics.
Author: Haiyan Xu
Author: Mark Chang
Author: Alex Dmitrienko
Author: Dan Lin
Author: Sandrine Dudoit
Author: Ying Lu
Author: 
Author: Thorsten Dickhaus
Author: Frank Bretz
Author: Ranajit Chakraborty