Download or read book Methods in Multiple Testing and Meta analysis with Applications to the Analysis of Genomic Data written by Yihan Li and published by . This book was released on 2014 with total page 160 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 Meta analysis and Combining Information in Genetics and Genomics written by Rudy Guerra and published by Chapman and Hall/CRC. This book was released on 2009-07-07 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: Novel Techniques for Analyzing and Combining Data from Modern Biological Studies Broadens the Traditional Definition of Meta-Analysis With the diversity of data and meta-data now available, there is increased interest in analyzing multiple studies beyond statistical approaches of formal meta-analysis. Covering an extensive range of quantitative information combination methods, Meta-analysis and Combining Information in Genetics and Genomics looks at how to analyze multiple studies from a broad perspective. After presenting the basic ideas and tools of meta-analysis, the book addresses the combination of similar data types: genotype data from genome-wide linkage scans and data derived from microarray gene expression experiments. The expert contributors show how some data combination problems can arise even within the same basic framework and offer solutions to these problems. They also discuss the combined analysis of different data types, giving readers an opportunity to see data combination approaches in action across a wide variety of genome-scale investigations. As heterogeneous data sets become more common, biological understanding will be significantly aided by jointly analyzing such data using fundamentally sound statistical methodology. This book provides many novel techniques for analyzing data from modern biological studies that involve multiple data sets, either of the same type or multiple data sources.
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 Meta Analysis and Combining Information in Genetics and Genomics written by Rudy Guerra and published by Chapman & Hall/CRC. This book was released on 2017-06-14 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: Novel Techniques for Analyzing and Combining Data from Modern Biological Studies Broadens the Traditional Definition of Meta-Analysis With the diversity of data and meta-data now available, there is increased interest in analyzing multiple studies beyond statistical approaches of formal meta-analysis. Covering an extensive range of quantitative information combination methods, Meta-analysis and Combining Information in Genetics and Genomicslooks at how to analyze multiple studies from a broad perspective. After presenting the basic ideas and tools of meta-analysis, the book addresses the combination of similar data types: genotype data from genome-wide linkage scans and data derived from microarray gene expression experiments. The expert contributors show how some data combination problems can arise even within the same basic framework and offer solutions to these problems. They also discuss the combined analysis of different data types, giving readers an opportunity to see data combination approaches in action across a wide variety of genome-scale investigations. As heterogeneous data sets become more common, biological understanding will be significantly aided by jointly analyzing such data using fundamentally sound statistical methodology. This book provides many novel techniques for analyzing data from modern biological studies that involve multiple data sets, either of the same type or multiple data sources.
Download or read book Meta Analysis written by Shahjahan Khan and published by Springer Nature. This book was released on 2020-10-27 with total page 294 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book focuses on performing hands-on meta-analysis using MetaXL, a free add-on to MS Excel. The illustrative examples are taken mainly from medical and health sciences studies, but the generic methods can be used to perform meta-analysis on data from any other discipline. The book adopts a step-by-step approach to perform meta-analyses and interpret the results. Stata codes for meta-analyses are also provided. All popularly used meta-analytic methods and models – such as the fixed effect model, random effects model, inverse variance heterogeneity model, and quality effect model – are used to find the confidence interval for the effect size measure of independent primary studies and the pooled study. In addition to the commonly used meta-analytic methods for various effect size measures, the book includes special topics such as meta-regression, dose-response meta-analysis, and publication bias. The main attraction for readers is the book’s simplicity and straightforwardness in conducting actual meta-analysis using MetaXL. Researchers would easily find everything on meta-analysis of any particular effect size in one specific chapter once they could determine the underlying effect measure. Readers will be able to see the results under different models and also will be able to select the correct model to obtain accurate results.
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 Estimation and Selection in High Dimensional Genomic Studies written by Hisashi Noma and published by Springer. This book was released on 2020-04-23 with total page 90 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides an overview of the statistical methods used in genome-wide screening of relevant genomic features or genes. Gene screening can facilitate deeper understanding of disease biology at the molecular level, possibly leading to discovery of new molecular targets for developing new treatments and developing diagnostic tests to predict patients’ prognosis or response to treatment. The most common approach to such gene screening studies is to apply multiple univariate analysis based on separate statistical tests for individual genes to test the null hypothesis of no association with clinical variables. This book first provides an overview of the state of the art of such multiple testing methodologies for gene screening, including frequentist multiple tests, empirical Bayes, and full-Bayes model-based methods for controlling the family-wise error rate or false discovery rate. Optimal discovery procedures and model-based variants are also discussed. Although great endeavor has been directed toward developing multiple testing methods, there are other, more relevant and effective analyses that should be given much attention in gene screening, including gene ranking, estimation of effect sizes, and classification accuracy based on selected genes. The core contents of this book provide a framework for integrated gene screening analysis based on hierarchical mixture modeling and empirical Bayes. Within this framework effective tools for multiple testing, ranking, estimation of effect size, and classification accuracy are derived. Methods for sample size determination for gene screening studies are also provided. With this content, the book is certain to expand the existing framework of statistical analysis based on multiple testing for gene screening to one based on estimation and selection.
Download or read book Individual Participant Data Meta Analysis written by Richard D. Riley and published by John Wiley & Sons. This book was released on 2021-06-08 with total page 38 pages. Available in PDF, EPUB and Kindle. Book excerpt: Individual Participant Data Meta-Analysis: A Handbook for Healthcare Research provides a comprehensive introduction to the fundamental principles and methods that healthcare researchers need when considering, conducting or using individual participant data (IPD) meta-analysis projects. Written and edited by researchers with substantial experience in the field, the book details key concepts and practical guidance for each stage of an IPD meta-analysis project, alongside illustrated examples and summary learning points. Split into five parts, the book chapters take the reader through the journey from initiating and planning IPD projects to obtaining, checking, and meta-analysing IPD, and appraising and reporting findings. The book initially focuses on the synthesis of IPD from randomised trials to evaluate treatment effects, including the evaluation of participant-level effect modifiers (treatment-covariate interactions). Detailed extension is then made to specialist topics such as diagnostic test accuracy, prognostic factors, risk prediction models, and advanced statistical topics such as multivariate and network meta-analysis, power calculations, and missing data. Intended for a broad audience, the book will enable the reader to: Understand the advantages of the IPD approach and decide when it is needed over a conventional systematic review Recognise the scope, resources and challenges of IPD meta-analysis projects Appreciate the importance of a multi-disciplinary project team and close collaboration with the original study investigators Understand how to obtain, check, manage and harmonise IPD from multiple studies Examine risk of bias (quality) of IPD and minimise potential biases throughout the project Understand fundamental statistical methods for IPD meta-analysis, including two-stage and one-stage approaches (and their differences), and statistical software to implement them Clearly report and disseminate IPD meta-analyses to inform policy, practice and future research Critically appraise existing IPD meta-analysis projects Address specialist topics such as effect modification, multiple correlated outcomes, multiple treatment comparisons, non-linear relationships, test accuracy at multiple thresholds, multiple imputation, and developing and validating clinical prediction models Detailed examples and case studies are provided throughout.
Download or read book MULTIPLE TESTING CORRECTION IN TIME SERIES ROLLING WINDOW ANALYSIS WITH APPLICATION OF GWAS METHODS written by and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract : Rolling window is a popular tool in time series analysis. When conducting hypothesis testing on each window simultaneously, multiple testing problem occurs. In the literature in rolling window analysis, it appears that bootstrap is the most frequently used, if not only, method to address the multiple testing issue. This thesis aims to adapt multiple testing correction methods that are popular in genome-wide association study to the time series rolling window context. In particular, some of these methods require the knowledge of the correlation structure of test statistics. In genetics, this structure can be obtained from an external source, which may not exist in time series. To overcome this difficulty, we adopt the AR sieve idea, which enables the computation of correlation structure based on the estimated AR coefficients. We also present the finite sample simulation to illustrate the performance of these methods.
Download or read book Analysis of Complex Disease Association Studies written by Eleftheria Zeggini and published by Academic Press. This book was released on 2010-11-17 with total page 353 pages. Available in PDF, EPUB and Kindle. Book excerpt: According to the National Institute of Health, a genome-wide association study is defined as any study of genetic variation across the entire human genome that is designed to identify genetic associations with observable traits (such as blood pressure or weight), or the presence or absence of a disease or condition. Whole genome information, when combined with clinical and other phenotype data, offers the potential for increased understanding of basic biological processes affecting human health, improvement in the prediction of disease and patient care, and ultimately the realization of the promise of personalized medicine. In addition, rapid advances in understanding the patterns of human genetic variation and maturing high-throughput, cost-effective methods for genotyping are providing powerful research tools for identifying genetic variants that contribute to health and disease. This burgeoning science merges the principles of statistics and genetics studies to make sense of the vast amounts of information available with the mapping of genomes. In order to make the most of the information available, statistical tools must be tailored and translated for the analytical issues which are original to large-scale association studies. Analysis of Complex Disease Association Studies will provide researchers with advanced biological knowledge who are entering the field of genome-wide association studies with the groundwork to apply statistical analysis tools appropriately and effectively. With the use of consistent examples throughout the work, chapters will provide readers with best practice for getting started (design), analyzing, and interpreting data according to their research interests. Frequently used tests will be highlighted and a critical analysis of the advantages and disadvantage complimented by case studies for each will provide readers with the information they need to make the right choice for their research. Additional tools including links to analysis tools, tutorials, and references will be available electronically to ensure the latest information is available. - Easy access to key information including advantages and disadvantage of tests for particular applications, identification of databases, languages and their capabilities, data management risks, frequently used tests - Extensive list of references including links to tutorial websites - Case studies and Tips and Tricks
Download or read book Computational Genomics with R written by Altuna Akalin and published by CRC Press. This book was released on 2020-12-16 with total page 463 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational Genomics with R provides a starting point for beginners in genomic data analysis and also guides more advanced practitioners to sophisticated data analysis techniques in genomics. The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background. This also contains practical and well-documented examples in R so readers can analyze their data by simply reusing the code presented. As the field of computational genomics is interdisciplinary, it requires different starting points for people with different backgrounds. For example, a biologist might skip sections on basic genome biology and start with R programming, whereas a computer scientist might want to start with genome biology. After reading: You will have the basics of R and be able to dive right into specialized uses of R for computational genomics such as using Bioconductor packages. You will be familiar with statistics, supervised and unsupervised learning techniques that are important in data modeling, and exploratory analysis of high-dimensional data. You will understand genomic intervals and operations on them that are used for tasks such as aligned read counting and genomic feature annotation. You will know the basics of processing and quality checking high-throughput sequencing data. You will be able to do sequence analysis, such as calculating GC content for parts of a genome or finding transcription factor binding sites. You will know about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization. You will be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq. You will know basic techniques for integrating and interpreting multi-omics datasets. Altuna Akalin is a group leader and head of the Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology, Max Delbrück Center, Berlin. He has been developing computational methods for analyzing and integrating large-scale genomics data sets since 2002. He has published an extensive body of work in this area. The framework for this book grew out of the yearly computational genomics courses he has been organizing and teaching since 2015.
Download or read book Big Data in Omics and Imaging written by Momiao Xiong and published by CRC Press. This book was released on 2017-12-01 with total page 595 pages. Available in PDF, EPUB and Kindle. Book excerpt: Big Data in Omics and Imaging: Association Analysis addresses the recent development of association analysis and machine learning for both population and family genomic data in sequencing era. It is unique in that it presents both hypothesis testing and a data mining approach to holistically dissecting the genetic structure of complex traits and to designing efficient strategies for precision medicine. The general frameworks for association analysis and machine learning, developed in the text, can be applied to genomic, epigenomic and imaging data. FEATURES Bridges the gap between the traditional statistical methods and computational tools for small genetic and epigenetic data analysis and the modern advanced statistical methods for big data Provides tools for high dimensional data reduction Discusses searching algorithms for model and variable selection including randomization algorithms, Proximal methods and matrix subset selection Provides real-world examples and case studies Will have an accompanying website with R code The book is designed for graduate students and researchers in genomics, bioinformatics, and data science. It represents the paradigm shift of genetic studies of complex diseases– from shallow to deep genomic analysis, from low-dimensional to high dimensional, multivariate to functional data analysis with next-generation sequencing (NGS) data, and from homogeneous populations to heterogeneous population and pedigree data analysis. Topics covered are: advanced matrix theory, convex optimization algorithms, generalized low rank models, functional data analysis techniques, deep learning principle and machine learning methods for modern association, interaction, pathway and network analysis of rare and common variants, biomarker identification, disease risk and drug response prediction.
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.
Download or read book Statistical Evidence written by Richard Royall and published by Routledge. This book was released on 2017-11-22 with total page 212 pages. Available in PDF, EPUB and Kindle. Book excerpt: Interpreting statistical data as evidence, Statistical Evidence: A Likelihood Paradigm focuses on the law of likelihood, fundamental to solving many of the problems associated with interpreting data in this way. Statistics has long neglected this principle, resulting in a seriously defective methodology. This book redresses the balance, explaining why science has clung to a defective methodology despite its well-known defects. After examining the strengths and weaknesses of the work of Neyman and Pearson and the Fisher paradigm, the author proposes an alternative paradigm which provides, in the law of likelihood, the explicit concept of evidence missing from the other paradigms. At the same time, this new paradigm retains the elements of objective measurement and control of the frequency of misleading results, features which made the old paradigms so important to science. The likelihood paradigm leads to statistical methods that have a compelling rationale and an elegant simplicity, no longer forcing the reader to choose between frequentist and Bayesian statistics.
Download or read book Doing Meta Analysis with R written by Mathias Harrer and published by CRC Press. This book was released on 2021-09-15 with total page 500 pages. Available in PDF, EPUB and Kindle. Book excerpt: Doing Meta-Analysis with R: A Hands-On Guide serves as an accessible introduction on how meta-analyses can be conducted in R. Essential steps for meta-analysis are covered, including calculation and pooling of outcome measures, forest plots, heterogeneity diagnostics, subgroup analyses, meta-regression, methods to control for publication bias, risk of bias assessments and plotting tools. Advanced but highly relevant topics such as network meta-analysis, multi-three-level meta-analyses, Bayesian meta-analysis approaches and SEM meta-analysis are also covered. A companion R package, dmetar, is introduced at the beginning of the guide. It contains data sets and several helper functions for the meta and metafor package used in the guide. The programming and statistical background covered in the book are kept at a non-expert level, making the book widely accessible. Features • Contains two introductory chapters on how to set up an R environment and do basic imports/manipulations of meta-analysis data, including exercises • Describes statistical concepts clearly and concisely before applying them in R • Includes step-by-step guidance through the coding required to perform meta-analyses, and a companion R package for the book
Download or read book Analysis of Longitudinal Data written by Peter Diggle and published by Oxford University Press, USA. This book was released on 2013-03-14 with total page 397 pages. Available in PDF, EPUB and Kindle. Book excerpt: This second edition has been completely revised and expanded to become the most up-to-date and thorough professional reference text in this fast-moving area of biostatistics. It contains an additional two chapters on fully parametric models for discrete repeated measures data and statistical models for time-dependent predictors.
