Gene Expression Studies Using Affymetrix Microarrays

Gene Expression Studies Using Affymetrix Microarrays

Author: Hinrich Gohlmann

Publisher: Chapman and Hall/CRC

Published: 2009-07-15

Total Pages: 0

ISBN-13: 9781420065152

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The Affymetrix GeneChip® system is one of the most widely adapted microarray platforms. However, due to the overwhelming amount of information available, many Affymetrix users tend to stick to the default analysis settings and may end up drawing sub-optimal conclusions. Written by a molecular biologist and a biostatistician with a combined decade of experience in practical expression profiling experiments and data analyses, Gene Expression Studies Using Affymetrix Microarrays tears down the omnipresent language barriers among molecular biology, bioinformatics, and biostatistics by explaining the entire process of a gene expression study from conception to conclusion. Truly Multidisciplinary: Merges Molecular Biology, Bioinformatics, and Biostatistics This authoritative resource covers important technical and statistical pitfalls and problems, helping not only to explain concepts outside the domain of researchers, but to provide additional guidance in their field of expertise. The book also describes technical and statistical methods conceptually with illustrative, full-color examples, enabling those inexperienced with gene expression studies to grasp the basic principles. Gene Expression Studies Using Affymetrix Microarrays provides novices with a detailed, yet focused introductory course and practical user guide. Specialized experts will also find it useful as a translation dictionary to understand other involved disciplines or to get a broader picture of microarray gene expression studies in general. Although focusing on Affymetrix gene expression, this globally relevant guide covers topics that are equally useful for other microarray platforms and other Affymetrix applications.


Gene Expression Studies Using Affymetrix Microarrays

Gene Expression Studies Using Affymetrix Microarrays

Author: Hinrich Gohlmann

Publisher: CRC Press

Published: 2009-07-15

Total Pages: 361

ISBN-13: 1420065165

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The Affymetrix GeneChip system is one of the most widely adapted microarray platforms. However, due to the overwhelming amount of information available, many Affymetrix users tend to stick to the default analysis settings and may end up drawing sub-optimal conclusions. Written by a molecular biologist and a biostatistician with a combined decade of


Microarray Gene Expression Data Analysis

Microarray Gene Expression Data Analysis

Author: Helen Causton

Publisher: John Wiley & Sons

Published: 2009-04-01

Total Pages: 176

ISBN-13: 1444311565

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This guide covers aspects of designing microarray experiments and analysing the data generated, including information on some of the tools that are available from non-commercial sources. Concepts and principles underpinning gene expression analysis are emphasised and wherever possible, the mathematics has been simplified. The guide is intended for use by graduates and researchers in bioinformatics and the life sciences and is also suitable for statisticians who are interested in the approaches currently used to study gene expression. Microarrays are an automated way of carrying out thousands of experiments at once, and allows scientists to obtain huge amounts of information very quickly Short, concise text on this difficult topic area Clear illustrations throughout Written by well-known teachers in the subject Provides insight into how to analyse the data produced from microarrays


Statistical Analysis of Gene Expression Microarray Data

Statistical Analysis of Gene Expression Microarray Data

Author: Terry Speed

Publisher: CRC Press

Published: 2003-03-26

Total Pages: 237

ISBN-13: 0203011236

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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


The Analysis of Gene Expression Data

The Analysis of Gene Expression Data

Author: Giovanni Parmigiani

Publisher: Springer Science & Business Media

Published: 2006-04-11

Total Pages: 511

ISBN-13: 0387216790

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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.


Encyclopedia of Molecular Pharmacology

Encyclopedia of Molecular Pharmacology

Author: Stefan Offermanns

Publisher: Springer Science & Business Media

Published: 2008-08-14

Total Pages: 1515

ISBN-13: 3540389164

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An essential text, this is a fully updated second edition of a classic, now in two volumes. It provides rapid access to information on molecular pharmacology for research scientists, clinicians and advanced students. With the A-Z format of over 2,000 entries, around 350 authors provide a complete reference to the area of molecular pharmacology. The book combines the knowledge of classic pharmacology with the more recent approach of the precise analysis of the molecular mechanisms by which drugs exert their effects. Short keyword entries define common acronyms, terms and phrases. In addition, detailed essays provide in-depth information on drugs, cellular processes, molecular targets, techniques, molecular mechanisms, and general principles.


Design and Analysis of DNA Microarray Investigations

Design and Analysis of DNA Microarray Investigations

Author: Richard M. Simon

Publisher: Springer Science & Business Media

Published: 2006-05-09

Total Pages: 205

ISBN-13: 0387218661

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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.


Bioarrays

Bioarrays

Author: Krishnarao Appasani

Publisher: Springer Science & Business Media

Published: 2007-10-04

Total Pages: 277

ISBN-13: 1597453285

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This book provides an integrated collection of timely articles on the use of bioarray techniques in the fields of biotechnology and molecular medicine. It is the first book to comprehensively integrate molecular diagnostics and molecular pathology. This book serves as an indispensable reference for graduate students, post-docs, and professors as well as an explanatory analysis for executives and scientists in biotechnology and pharmaceutical companies.


Large-Scale Inference

Large-Scale Inference

Author: Bradley Efron

Publisher: Cambridge University Press

Published: 2012-11-29

Total Pages:

ISBN-13: 1139492136

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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.


Batch Effects and Noise in Microarray Experiments

Batch Effects and Noise in Microarray Experiments

Author: Andreas Scherer

Publisher: John Wiley & Sons

Published: 2009-11-03

Total Pages: 272

ISBN-13: 9780470685990

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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.