Biologist's Guide to Analysis of DNA Microarray Data

by Steen Knudsen

Publisher: John Wiley & Sons; 1st Edition
ISBN: 0471224901

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From Book News, Inc.

A text for students and scientists new to DNA array data analysis, written for biologists without special training in data analysis and statistics. Knudsen (Technical U. of Denmark) covers the spectrum of established analysis approaches, including cluster analysis, function prediction, and principal component analysis. He also reviews software programs and discusses criteria for selecting programs.

Book Description

Microarrays are low-density arrays of DNA molecules that permit many hybridization experiments to be performed in parallel. A Biologist's Guide to Analysis of DNA Microarray Data is the first authoritative text to focus on analysis (as opposed to technology) in diverse biological and medical applications of microarrays.

Written for biologists without special training in data analysis and statistics, the Guide takes over where the image analysis software that accompanies DNA array equipment typically leaves off-with a file of signal intensities and fold changes compared to a control. The broad spectrum of established analysis approaches is covered, including cluster analysis, function prediction, and principal component analysis. A thorough, critical review of software programs is presented, and criteria for selecting programs are discussed. Each chapter contains a Further Reading section categorized by topic as well as a summary, and highlights numerous real examples to illustrate the key concepts. Chapter topics include:

• Basic data analysis
• Visualization by reduction of dimensionality
• Cluster analysis of expression data
• Molecular classifiers
• Genotyping chips
• Software issues and data formats

A Biologist's Guide to Analysis of DNA Microarray Data meets the needs of research professionals, students, and trainees alike for a compact yet thorough guide to analyzing microarray data.

From the Author

DNA microarrays represent an exponentially growing technology that is revolutionizing biology, medicine and the pharmaceutical industry. As new applications for this technology are found every day, it is important to train future scientists and existing users in how to use the technology efficiently and correctly. This book is an important step in that direction. Without assuming any special knowledge in statistics or bioinformatics, it explains the most common methods used for analyzing DNA microarray data with an emphasis on expression arrays. Each chapter is also supplemented with simple examples and sections on Further Reading that categorize the relevant literature by topic.

Customer Review

This is the best short introduction that I've seen to DNA microarray analysis - and our lab has just about every computational biology book ever published. (We are the core array analysis facility at the U of Colorado School of Medicine, operating downstream of one of the largest single Affymetrix facilities in academia.)

This book is clear, accurate, and concise - I'm very enthusiastic about it. I've recommended it to everyone in our lab, and to our collaborators. I have even xeroxed the analysis flow chart in fig 2.1, annotated it a bit, and taped it on our lab door. I found something I really liked on just about every other page. One example: the comparison between Euclidean and Pearson correlation distance on pp. 45-46 is the best short explanation I have ever seen.

Chapter 2 on basic data analysis is superb (it even manages to describe the Multiple Testing problem in its limited number of pages), and the chapters on investigating regulatory nets and molecular classifiers give you a wonderful taste of some cutting-edge stuff within their length constraints. All the chapters are excellent. Biblio is very current. Price is a little steep ... for ~150 pages, but it's a great little book. 5 stars.