Batch Effects and Noise in Microarray Experiments PDF Download
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Author: Andreas Scherer
Publisher: John Wiley & Sons
ISBN: 9780470685990
Category : Science
Languages : en
Pages : 272
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Book Description
Batch Effects and Noise in Microarray Experiments: Sources and Solutions looks at the issue of technical noise and batch effects in microarray studies and illustrates how to alleviate such factors whilst interpreting the relevant biological information. Each chapter focuses on sources of noise and batch effects before starting an experiment, with examples of statistical methods for detecting, measuring, and managing batch effects within and across datasets provided online. Throughout the book the importance of standardization and the value of standard operating procedures in the development of genomics biomarkers is emphasized. Key Features: A thorough introduction to Batch Effects and Noise in Microrarray Experiments. A unique compilation of review and research articles on handling of batch effects and technical and biological noise in microarray data. An extensive overview of current standardization initiatives. All datasets and methods used in the chapters, as well as colour images, are available on www.the-batch-effect-book.org, so that the data can be reproduced. An exciting compilation of state-of-the-art review chapters and latest research results, which will benefit all those involved in the planning, execution, and analysis of gene expression studies.
Author: Andreas Scherer
Publisher: John Wiley & Sons
ISBN: 9780470685990
Category : Science
Languages : en
Pages : 272
Get Book Here
Book Description
Batch Effects and Noise in Microarray Experiments: Sources and Solutions looks at the issue of technical noise and batch effects in microarray studies and illustrates how to alleviate such factors whilst interpreting the relevant biological information. Each chapter focuses on sources of noise and batch effects before starting an experiment, with examples of statistical methods for detecting, measuring, and managing batch effects within and across datasets provided online. Throughout the book the importance of standardization and the value of standard operating procedures in the development of genomics biomarkers is emphasized. Key Features: A thorough introduction to Batch Effects and Noise in Microrarray Experiments. A unique compilation of review and research articles on handling of batch effects and technical and biological noise in microarray data. An extensive overview of current standardization initiatives. All datasets and methods used in the chapters, as well as colour images, are available on www.the-batch-effect-book.org, so that the data can be reproduced. An exciting compilation of state-of-the-art review chapters and latest research results, which will benefit all those involved in the planning, execution, and analysis of gene expression studies.
Author: Andreas Scherer
Publisher: John Wiley & Sons
ISBN: 0470741384
Category : Science
Languages : en
Pages : 292
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Book Description
Batch Effects and Noise in Microarray Experiments: Sources and Solutions looks at the issue of technical noise and batch effects in microarray studies and illustrates how to alleviate such factors whilst interpreting the relevant biological information. Each chapter focuses on sources of noise and batch effects before starting an experiment, with examples of statistical methods for detecting, measuring, and managing batch effects within and across datasets provided online. Throughout the book the importance of standardization and the value of standard operating procedures in the development of genomics biomarkers is emphasized. Key Features: A thorough introduction to Batch Effects and Noise in Microrarray Experiments. A unique compilation of review and research articles on handling of batch effects and technical and biological noise in microarray data. An extensive overview of current standardization initiatives. All datasets and methods used in the chapters, as well as colour images, are available on www.the-batch-effect-book.org, so that the data can be reproduced. An exciting compilation of state-of-the-art review chapters and latest research results, which will benefit all those involved in the planning, execution, and analysis of gene expression studies.
Author: Giovanni Parmigiani
Publisher: Springer Science & Business Media
ISBN: 0387216790
Category : Medical
Languages : en
Pages : 511
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Book Description
This book presents practical approaches for the analysis of data from gene expression micro-arrays. It describes the conceptual and methodological underpinning for a statistical tool and its implementation in software. The book includes coverage of various packages that are part of the Bioconductor project and several related R tools. The materials presented cover a range of software tools designed for varied audiences.
Author: Richard M. Simon
Publisher: Springer Science & Business Media
ISBN: 0387218661
Category : Medical
Languages : en
Pages : 205
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Book Description
The analysis of gene expression profile data from DNA micorarray studies are discussed in this book. It provides a review of available methods and presents it in a manner that is intelligible to biologists. It offers an understanding of the design and analysis of experiments utilizing microarrays to benefit scientists. It includes an Appendix tutorial on the use of BRB-ArrayTools and step by step analyses of several major datasets using this software which is available from the National Cancer Institute.
Author: Terry Speed
Publisher: CRC Press
ISBN: 0203011236
Category : Mathematics
Languages : en
Pages : 237
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Book Description
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
Author: Robert Gentleman
Publisher: Springer Science & Business Media
ISBN: 0387293620
Category : Computers
Languages : en
Pages : 478
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Book Description
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.
Author: Edmund R. Malinowski
Publisher: John Wiley & Sons
ISBN:
Category : Mathematics
Languages : en
Pages : 280
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Book Description
Good,No Highlights,No Markup,all pages are intact, Slight Shelfwear,may have the corners slightly dented, may have slight color changes/slightly damaged spine.
Author: Florian Hahne
Publisher: Springer Science & Business Media
ISBN: 0387772405
Category : Science
Languages : en
Pages : 287
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Book Description
Bioconductor software has become a standard tool for the analysis and comprehension of data from high-throughput genomics experiments. Its application spans a broad field of technologies used in contemporary molecular biology. In this volume, the authors present a collection of cases to apply Bioconductor tools in the analysis of microarray gene expression data. Topics covered include: (1) import and preprocessing of data from various sources; (2) statistical modeling of differential gene expression; (3) biological metadata; (4) application of graphs and graph rendering; (5) machine learning for clustering and classification problems; (6) gene set enrichment analysis. Each chapter of this book describes an analysis of real data using hands-on example driven approaches. Short exercises help in the learning process and invite more advanced considerations of key topics. The book is a dynamic document. All the code shown can be executed on a local computer, and readers are able to reproduce every computation, figure, and table.
Author: William Evan Johnson
Publisher:
ISBN: 9780549039969
Category :
Languages : en
Pages : 167
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Book Description
This work is a presentation of novel statistical methods for preprocessing and downstream analysis of data from applications on microarrays. One topic discussed in this work is a method for preprocessing microarray data for non-biological variation, or batch effects, which are commonly observed across multiple batches of microarray experiments. The ability to combine microarray data sets is advantageous to researchers to increase statistical power in studies where logistical considerations restrict sample size or require the sequential hybridization of arrays. In this work, parametric and nonparametric empirical Bayes frameworks are presented for adjusting data for batch effects that are robust to outliers in small sample sizes. The method is illustrated using example data sets and show that the method is justifiable and useful in practice.
Author: Rune Matthiesen
Publisher:
ISBN: 9781627033923
Category : Mass spectrometry
Languages : en
Pages : 405
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Book Description
Since the publishing of the first edition, the methodologies and instrumentation involved in the field of mass spectrometry-based proteomics has improved considerably. Fully revised and expanded, Mass Spectrometry Data Analysis in Proteomics, Second Edition presents expert chapters on specific MS-based methods or data analysis strategies in proteomics. The volume covers data analysis topics relevant for quantitative proteomics, post translational modification, HX-MS, glycomics, and data exchange standards, among other topics. Written in the highly successful Methods in Molecular Biology series format, chapters include brief introductions to their respective subjects, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Updated and authoritative, Mass Spectrometry Data Analysis in Proteomics, Second Edition serves as a detailed guide for all researchers seeking to further our knowledge in the field of proteomics.
