Download or read book Controlling Error Rates with Multiple Positively dependent Tests written by Abdullah Al Masud and published by . This book was released on 2011 with total page 75 pages. Available in PDF, EPUB and Kindle. Book excerpt: It is a typical feature of high dimensional data analysis, for example a microarray study, that a researcher allows thousands of statistical tests at a time. All inferences for the tests are determined using the p-values; a smaller p-value than the alpha-level It is a typical feature of high dimensional data analysis, for example a microarray study, that a researcher allows thousands of statistical tests at a time. All inferences for the tests are determined using the p-values; a smaller p-value than the -level of the test signifies a statistically significant test. As the number of tests increases, the chance of observing some small p-values is very high even when all null hypotheses are true. Consequently, we make wrong conclusions on the hypotheses. This type of potential problem frequently happens when we test several hypotheses simultaneously, i.e., the multiple testing problem. Adjustment of the p-values can redress the problem that arises in multiple hypothesis testing. P-value adjustment methods control error rates [type I error (i.e. false positive) and type II error (i.e. false negative)] for each hypothesis in order to achieve high statistical power while keeping the overall Family Wise Error Rate (FWER) no larger than, where is most often set to 0.05. However, researchers also consider the False Discovery Rate (FDR), or Positive False Discovery Rate (pFDR) instead of the type I error in multiple comparison problems for microarray studies. The methods involved in controlling the FDR always provide higher statistical power than the methods involved in controlling the type I error rate while keeping the type II error rate low. In practice, microarray studies involve dependent test statistics (or p-values) because genes can be fully dependent on each other in a complicated biological structure. However, some of the p-value adjustment methods only deal with independent test statistics. Thus, we carry out a simulation study with several methods involved in multiple hypothesis testing. Our result suggests a suitable method given that the test statistics are dependent with a particular covariance structure while allowing different values of the underlying parameters in the alternative hypotheses.
Download or read book A Manual of the History of Dogmas written by Bernard John Otten and published by . This book was released on 1917 with total page 554 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 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 Familywise Robustness Criteria Revisited for Newer Multiple Testing Procedures written by Charles W. Miller and published by . This book was released on 2009 with total page 101 pages. Available in PDF, EPUB and Kindle. Book excerpt: As the availability of large datasets becomes more prevalent, so does the need to discover significant findings among a large collection of hypotheses. Multiple testing procedures (MTP) are used to control the familywise error rate (FWER) or the chance to commit at least one type I error when performing multiple hypotheses testing. When controlling the FWER, the power of a MTP to detect significant differences decreases as the number of hypotheses increases. It would be ideal to discover the same false null hypotheses despite the family of hypotheses chosen to be tested. Holland and Cheung (2002) developed measures called familywise robustness criteria (FWR) to study the effect of family size on the acceptance and rejection of a hypothesis. Their analysis focused on procedures that controlled FWER and false discovery rate (FDR). Newer MTPs have since been developed which control the generalized FWER (gFWER (k) or k-FWER) and false discovery proportion (FDP) or tail probabilities for the proportion of false positives (TPPFP). This dissertation reviews these newer procedures and then discusses the effect of family size using the FWRs of Holland and Cheung. In the case where the test statistics are independent and the null hypotheses are all true, the Type R enlargement familywise robustness measure can be expressed as a ratio of the expected number of Type I errors. In simulations, positive dependence among the test statistics was introduced, the expected number of Type I errors and the Type R enlargement FWR increased for step-up procedures with higher levels of correlation, but not for step-down or single-step procedures.
Download or read book New Step Down Procedures for Control of the Familywise Error Rate written by Zijiang Yang and published by . This book was released on 2008 with total page 91 pages. Available in PDF, EPUB and Kindle. Book excerpt: The main research topic in this dissertation is the development of the closure method of multiple testing procedures. Considering a general procedure that allows the underlying test statistics as well as the associated parameters to be dependent, we first propose a step-down procedure controlling the FWER, which is defined as the probability of committing at least one false discovery. Holm (1979) first proposed a step-down procedure for multiple hypothesis testing with a control of the familywise error rate (FWER) under any kind of dependence. Under the normal distributional setup, Seneta and Chen (2005) sharpened the Holm procedure by taking into account the correlations between the test statistics. In this dissertation, the Seneta-Chen procedure is further modified yielding a more powerful FWER controlling procedure. We then advance our research and propose another step-down procedure to control the generalized FWER (k-FWER), which is defined as the probability of making at least k false discoveries. We compare our proposed k-FWER procedure with the Lehmann and Romano (2005) procedure. The proposed k-FWER procedure is more powerful, particularly when there is a strong dependence in the tests. When the proportion of true null hypotheses is expected to be small, the traditional tests are usually conservative by a factor associated with pi0, which is the proportion of true null hypotheses among all null hypotheses. Under independence, two procedures controlling the FWER and the k-FWER are proposed in this dissertation. Simulations are carried out to show that our procedures often provide much better FWER or k-FWER control and power than the traditional procedures.
Download or read book Multiple Comparison Procedures written by Yosef Hochberg and published by . This book was released on 1987-10-05 with total page 482 pages. Available in PDF, EPUB and Kindle. Book excerpt: Offering a balanced, up-to-date view of multiple comparison procedures, this book refutes the belief held by some statisticians that such procedures have no place in data analysis. With equal emphasis on theory and applications, it establishes the advantages of multiple comparison techniques in reducing error rates and in ensuring the validity of statistical inferences. Provides detailed descriptions of the derivation and implementation of a variety of procedures, paying particular attention to classical approaches and confidence estimation procedures. Also discusses the benefits and drawbacks of other methods. Numerous examples and tables for implementing procedures are included, making this work both practical and informative.
Download or read book Handbook of Multiple Comparisons written by Xinping Cui and published by CRC Press. This book was released on 2021-11-18 with total page 418 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by experts that include originators of some key ideas, chapters in the Handbook of Multiple Testing cover multiple comparison problems big and small, with guidance toward error rate control and insights on how principles developed earlier can be applied to current and emerging problems. Some highlights of the coverages are as follows. Error rate control is useful for controlling the incorrect decision rate. Chapter 1 introduces Tukey's original multiple comparison error rates and point to how they have been applied and adapted to modern multiple comparison problems as discussed in the later chapters. Principles endure. While the closed testing principle is more familiar, Chapter 4 shows the partitioning principle can derive confidence sets for multiple tests, which may become important as the profession goes beyond making decisions based on p-values. Multiple comparisons of treatment efficacy often involve multiple doses and endpoints. Chapter 12 on multiple endpoints explains how different choices of endpoint types lead to different multiplicity adjustment strategies, while Chapter 11 on the MCP-Mod approach is particularly useful for dose-finding. To assess efficacy in clinical trials with multiple doses and multiple endpoints, the reader can see the traditional approach in Chapter 2, the Graphical approach in Chapter 5, and the multivariate approach in Chapter 3. Personalized/precision medicine based on targeted therapies, already a reality, naturally leads to analysis of efficacy in subgroups. Chapter 13 draws attention to subtle logical issues in inferences on subgroups and their mixtures, with a principled solution that resolves these issues. This chapter has implication toward meeting the ICHE9R1 Estimands requirement. Besides the mere multiple testing methodology itself, the handbook also covers related topics like the statistical task of model selection in Chapter 7 or the estimation of the proportion of true null hypotheses (or, in other words, the signal prevalence) in Chapter 8. It also contains decision-theoretic considerations regarding the admissibility of multiple tests in Chapter 6. The issue of selected inference is addressed in Chapter 9. Comparison of responses can involve millions of voxels in medical imaging or SNPs in genome-wide association studies (GWAS). Chapter 14 and Chapter 15 provide state of the art methods for large scale simultaneous inference in these settings.
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.
Download or read book Recent Advances In Biostatistics False Discovery Rates Survival Analysis And Related Topics written by Manish C Bhattacharjee and published by World Scientific. This book was released on 2011-03-18 with total page 311 pages. Available in PDF, EPUB and Kindle. Book excerpt: This unique volume provides self-contained accounts of some recent trends in Biostatistics methodology and their applications. It includes state-of-the-art reviews and original contributions.The articles included in this volume are based on a careful selection of peer-reviewed papers, authored by eminent experts in the field, representing a well balanced mix of researchers from the academia, R&D sectors of government and the pharmaceutical industry.The book is also intended to give advanced graduate students and new researchers a scholarly overview of several research frontiers in biostatistics, which they can use to further advance the field through development of new techniques and results.
Download or read book Medical Biostatistics for Complex Diseases written by Frank Emmert-Streib and published by John Wiley & Sons. This book was released on 2010-03-30 with total page 412 pages. Available in PDF, EPUB and Kindle. Book excerpt: A collection of highly valuable statistical and computational approaches designed for developing powerful methods to analyze large-scale high-throughput data derived from studies of complex diseases. Such diseases include cancer and cardiovascular disease, and constitute the major health challenges in industrialized countries. They are characterized by the systems properties of gene networks and their interrelations, instead of individual genes, whose malfunctioning manifests in pathological phenotypes, thus making the analysis of the resulting large data sets particularly challenging. This is why novel approaches are needed to tackle this problem efficiently on a systems level. Written by computational biologists and biostatisticians, this book is an invaluable resource for a large number of researchers working on basic but also applied aspects of biomedical data analysis emphasizing the pathway level.
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 On Group Sequential Multiple Testing Controlling Familywise Error Rate written by Yiyong Fu and published by . This book was released on 2015 with total page 122 pages. Available in PDF, EPUB and Kindle. Book excerpt: The importance of multiplicity adjustment has gained wide recognition in modern scientific research. Without it, there will be too many spurious results and reproducibility becomes an issue; with it, if overtly conservative, discoveries will be made more difficult. In the current literature on repeated testing of multiple hypotheses, Bonferroni-based methods are still the main vehicle carrying the bulk of multiplicity adjustment. There is room for power improvement by suitably utilizing both hypothesis-wise and analysis- wise dependencies. This research will contribute to the development of a natural group-sequential extension of the classical stepwise multiple testing procedures, such as Dunnett's stepdown and Hochberg's step-up procedures. It is shown that the proposed group-sequential procedures strongly control the familywise error rate while being more powerful than the recently developed class of group-sequential Bonferroni-Holm's procedures. Particularly in this research, a convexity property is discovered for the distribution of the maxima of pairwise null P-values with the underlying test statistics having distributions such as bivariate normal, t, Gamma, F, or Archimedean copulas. Such property renders itself for an immediate use in improving Holm's procedure by incorporating pairwise dependencies of P-values. The improved Holm's procedure, as all stepdown multiple testing procedures, can also be naturally extended to group-sequential setting.
Download or read book Statistical Issues in Drug Development written by Stephen S. Senn and published by John Wiley & Sons. This book was released on 2008-02-28 with total page 523 pages. Available in PDF, EPUB and Kindle. Book excerpt: Drug development is the process of finding and producingtherapeutically useful pharmaceuticals, turning them into safe andeffective medicine, and producing reliable information regardingthe appropriate dosage and dosing intervals. With regulatoryauthorities demanding increasingly higher standards in suchdevelopments, statistics has become an intrinsic and criticalelement in the design and conduct of drug development programmes. Statistical Issues in Drug Development presents anessential and thought provoking guide to the statistical issues andcontroversies involved in drug development. This highly readable second edition has been updated toinclude: Comprehensive coverage of the design and interpretation ofclinical trials. Expanded sections on missing data, equivalence, meta-analysisand dose finding. An examination of both Bayesian and frequentist methods. A new chapter on pharmacogenomics and expanded coverage ofpharmaco-epidemiology and pharmaco-economics. Coverage of the ICH guidelines, in particular ICH E9,Statistical Principles for Clinical Trials. It is hoped that the book will stimulate dialogue betweenstatisticians and life scientists working within the pharmaceuticalindustry. The accessible and wide-ranging coverage make itessential reading for both statisticians and non-statisticiansworking in the pharmaceutical industry, regulatory bodies andmedical research institutes. There is also much to benefitundergraduate and postgraduate students whose courses include amedical statistics component.
Download or read book Large Scale Inference written by Bradley Efron and published by Cambridge University Press. This book was released on 2012-11-29 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: We live in a new age for statistical inference, where modern scientific technology such as microarrays and fMRI machines routinely produce thousands and sometimes millions of parallel data sets, each with its own estimation or testing problem. Doing thousands of problems at once is more than repeated application of classical methods. Taking an empirical Bayes approach, Bradley Efron, inventor of the bootstrap, shows how information accrues across problems in a way that combines Bayesian and frequentist ideas. Estimation, testing and prediction blend in this framework, producing opportunities for new methodologies of increased power. New difficulties also arise, easily leading to flawed inferences. This book takes a careful look at both the promise and pitfalls of large-scale statistical inference, with particular attention to false discovery rates, the most successful of the new statistical techniques. Emphasis is on the inferential ideas underlying technical developments, illustrated using a large number of real examples.
Download or read book Understanding Statistics and Experimental Design written by Michael H. Herzog and published by Springer. This book was released on 2019-08-13 with total page 146 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access textbook provides the background needed to correctly use, interpret and understand statistics and statistical data in diverse settings. Part I makes key concepts in statistics readily clear. Parts I and II give an overview of the most common tests (t-test, ANOVA, correlations) and work out their statistical principles. Part III provides insight into meta-statistics (statistics of statistics) and demonstrates why experiments often do not replicate. Finally, the textbook shows how complex statistics can be avoided by using clever experimental design. Both non-scientists and students in Biology, Biomedicine and Engineering will benefit from the book by learning the statistical basis of scientific claims and by discovering ways to evaluate the quality of scientific reports in academic journals and news outlets.
Download or read book Control of Generalized Error Rates in Multiple Testing written by Joseph P. Romano and published by . This book was released on 2005 with total page 50 pages. Available in PDF, EPUB and Kindle. Book excerpt:
