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Resampling Based Multiple Testing
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Book Synopsis Resampling-Based Multiple Testing by : Peter H. Westfall
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.
Book Synopsis Resampling-based Multiple Testing with Applications to Microarray Data Analysis by : Dongmei Li
Download or read book Resampling-based Multiple Testing with Applications to Microarray Data Analysis written by Dongmei Li and published by . This book was released on 2009 with total page 120 pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract: In microarray data analysis, resampling methods are widely used to discover significantly differentially expressed genes under different biological conditions when the distributions of test statistics are unknown. When sample size is small, however, simultaneous testing of thousands, or even millions, of null hypotheses in microarray data analysis brings challenges to the multiple hypothesis testing field. We study small sample behavior of three commonly used resampling methods, including permutation tests, post-pivot resampling methods, and pre-pivot resampling methods in multiple hypothesis testing. We show the model-based pre-pivot resampling methods have the largest maximum number of unique resampled test statistic values, which tend to produce more reliable P-values than the other two resampling methods. To avoid problems with the application of the three resampling methods in practice, we propose new conditions, based on the Partitioning Principle, to control the multiple testing error rates in fixed-effects general linear models. Meanwhile, from both theoretical results and simulation studies, we show the discrepancies between the true expected values of order statistics and the expected values of order statistics estimated by permutation in the Significant Analysis of Microarrays (SAM) procedure. Moreover, we show the conditions for SAM to control the expected number of false rejections in the permutation-based SAM procedure. We also propose a more powerful adaptive two-step procedure to control the expected number of false rejections with larger critical values than the Bonferroni procedure.
Book Synopsis Multiple Testing Procedures with Applications to Genomics by : Sandrine Dudoit
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.
Book Synopsis Modelling and Resampling Based Multiple Testing with Applications to Genetics by : Yifan Huang
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.
Book Synopsis Multiple Comparisons Using R by : Frank Bretz
Download or read book Multiple Comparisons Using R written by Frank Bretz and published by CRC Press. This book was released on 2016-04-19 with total page 202 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Multiple Testing Problems in Pharmaceutical Statistics by : Alex Dmitrienko
Download or read book Multiple Testing Problems in Pharmaceutical Statistics written by Alex Dmitrienko and published by CRC Press. This book was released on 2009-12-08 with total page 323 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Download or read book Permutation Tests written by Phillip Good and published by Springer Science & Business Media. This book was released on 2013-04-17 with total page 288 pages. Available in PDF, EPUB and Kindle. Book excerpt: A step-by-step manual on the application of permutation tests in biology, business, medicine, science, and engineering. Its intuitive and informal style make it ideal for students and researchers, whether experienced or coming to these resampling methods for the first time. The real-world problems of missing and censored data, multiple comparisons, nonresponders, after-the-fact covariates, and outliers are all dealt with at length. This new edition has more than 100 additional pages, and includes streamlined statistics for the k-sample comparison and analysis of variance plus expanded sections on computational techniques, multiple comparisons, multiple regression, comparing variances, and testing interactions in balanced designs. The comprehensive author and subject indexes, plus an expert-system guide to methods, provide for further ease of use, while the exercises at the end of every chapter have been supplemented with drills and a number of graduate-level thesis problems.
Book Synopsis Stepwise Multiple Testing as Formalized Data Snooping by : Michael Wolf
Download or read book Stepwise Multiple Testing as Formalized Data Snooping written by Michael Wolf and published by . This book was released on 2011 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: It is common in econometric applications that several hypothesis tests are carried out at the same time. The problem then becomes how to decide which hypotheses to reject, accounting for the multitude of tests. In this paper, we suggest a stepwise multiple testing procedure which asymptotically controls the familywise error rate at a desired level. Compared to related single-step methods, our procedure is more powerful in the sense that it often will reject more false hypotheses. Unlike some stepwise methods, our method implicitly captures the joint dependence structure of the test statistics, which results in increased ability to detect alternative hypotheses. We prove our method asymptotically controls the familywise error rate under minimal assumptions. Some simulation studies show the improvements of our methods over previous proposals. We also provide an application to a set of real data.
Book Synopsis Resampling-based Methods for Multiple Hypothesis Testing by : Jennifer A. Schumi
Download or read book Resampling-based Methods for Multiple Hypothesis Testing written by Jennifer A. Schumi and published by . This book was released on 2006 with total page 188 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Permutation Tests written by Phillip Good and published by Springer Science & Business Media. This book was released on 2013-03-09 with total page 238 pages. Available in PDF, EPUB and Kindle. Book excerpt: A step-by-step guide to the application of permutation tests in biology, medicine, science, and engineering. The intuitive and informal style makes this manual ideally suitable for students and researchers approaching these methods for the first time. In particular, it shows how to handle the problems of missing and censored data, nonresponders, after-the-fact covariates, and outliers.
Book Synopsis Bioinformatics and Computational Biology Solutions Using R and Bioconductor by : Robert Gentleman
Download or read book Bioinformatics and Computational Biology Solutions Using R and Bioconductor written by Robert Gentleman and published by Springer Science & Business Media. This book was released on 2005-12-29 with total page 478 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Efficient Computation of Adjusted P-Values for Resampling-Based Stepdown Multiple Testing by : Joseph P. Romano
Download or read book Efficient Computation of Adjusted P-Values for Resampling-Based Stepdown Multiple Testing written by Joseph P. Romano and published by . This book was released on 2016 with total page 7 pages. Available in PDF, EPUB and Kindle. Book excerpt: There has been a recent interest in reporting p-values adjusted for resampling-based stepdown multiple testing procedures proposed in Romano and Wolf (2005a,b). The original papers only describe how to carry out multiple testing at a fixed significance level. Computing adjusted p-values instead in an efficient manner is not entirely trivial. Therefore, this paper fills an apparent gap by detailing such an algorithm.
Book Synopsis Multiple Comparisons and Multiple Tests by : Peter H. Westfall
Download or read book Multiple Comparisons and Multiple Tests written by Peter H. Westfall and published by SAS Press. This book was released on 2000 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Does your work require multiple inferences? Are you a statistics teacher looking for a study guide to supplement the usually incomplete or outdated multiple comparisons/multiple testing material in your textbook? This workbook, the companion guide written specifically for use with Multiple Comparisons and Multiple Tests Using the SAS System, provides the supplement you need. Use this workbook and you will find problems and solutions that will enhance your understanding of the material within the main text. The workbook also provides updated information about multiple comparisons procedures, including enhancements for Release 8.1 of the SAS System. The chapters correlate with the chapters of the main text, and the format is clear and easy to use. This book and the companion text are quite useful as supplements for learning multiple comparisons procedures in standard linear models, multivariate analysis, categorical analysis, and regression and nonparametric statistics. Book jacket.
Book Synopsis Introductory Statistics and Analytics by : Peter C. Bruce
Download or read book Introductory Statistics and Analytics written by Peter C. Bruce and published by John Wiley & Sons. This book was released on 2015-01-08 with total page 320 pages. Available in PDF, EPUB and Kindle. Book excerpt: Concise, thoroughly class-tested primer that features basic statistical concepts in the concepts in the context of analytics, resampling, and the bootstrap A uniquely developed presentation of key statistical topics, Introductory Statistics and Analytics: A Resampling Perspective provides an accessible approach to statistical analytics, resampling, and the bootstrap for readers with various levels of exposure to basic probability and statistics. Originally class-tested at one of the first online learning companies in the discipline, www.statistics.com, the book primarily focuses on applications of statistical concepts developed via resampling, with a background discussion of mathematical theory. This feature stresses statistical literacy and understanding, which demonstrates the fundamental basis for statistical inference and demystifies traditional formulas. The book begins with illustrations that have the essential statistical topics interwoven throughout before moving on to demonstrate the proper design of studies. Meeting all of the Guidelines for Assessment and Instruction in Statistics Education (GAISE) requirements for an introductory statistics course, Introductory Statistics and Analytics: A Resampling Perspective also includes: Over 300 “Try It Yourself” exercises and intermittent practice questions, which challenge readers at multiple levels to investigate and explore key statistical concepts Numerous interactive links designed to provide solutions to exercises and further information on crucial concepts Linkages that connect statistics to the rapidly growing field of data science Multiple discussions of various software systems, such as Microsoft Office Excel®, StatCrunch, and R, to develop and analyze data Areas of concern and/or contrasting points-of-view indicated through the use of “Caution” icons Introductory Statistics and Analytics: A Resampling Perspective is an excellent primary textbook for courses in preliminary statistics as well as a supplement for courses in upper-level statistics and related fields, such as biostatistics and econometrics. The book is also a general reference for readers interested in revisiting the value of statistics.
Book Synopsis Feature Engineering and Selection by : Max Kuhn
Download or read book Feature Engineering and Selection written by Max Kuhn and published by CRC Press. This book was released on 2019-07-25 with total page 266 pages. Available in PDF, EPUB and Kindle. Book excerpt: The process of developing predictive models includes many stages. Most resources focus on the modeling algorithms but neglect other critical aspects of the modeling process. This book describes techniques for finding the best representations of predictors for modeling and for nding the best subset of predictors for improving model performance. A variety of example data sets are used to illustrate the techniques along with R programs for reproducing the results.
Book Synopsis Multiple Hypothesis Testing by : Houston Nash Gilbert
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:
Book Synopsis Monte Carlo Simulation and Resampling Methods for Social Science by : Thomas M. Carsey
Download or read book Monte Carlo Simulation and Resampling Methods for Social Science written by Thomas M. Carsey and published by SAGE Publications. This book was released on 2013-08-05 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt: Taking the topics of a quantitative methodology course and illustrating them through Monte Carlo simulation, this book examines abstract principles, such as bias, efficiency, and measures of uncertainty in an intuitive, visual way. Instead of thinking in the abstract about what would happen to a particular estimator "in repeated samples," the book uses simulation to actually create those repeated samples and summarize the results. The book includes basic examples appropriate for readers learning the material for the first time, as well as more advanced examples that a researcher might use to evaluate an estimator he or she was using in an actual research project. The book also covers a wide range of topics related to Monte Carlo simulation, such as resampling methods, simulations of substantive theory, simulation of quantities of interest (QI) from model results, and cross-validation. Complete R code from all examples is provided so readers can replicate every analysis presented using R.
