DNA Microarrays and Related Genomics Techniques: Design, Analysis, and Interpretation of Experiments

by Allison; David B.

• ISBN13: 9780824754617
• ISBN10: 0824754611
• Edition: 1st
• Format: Hardcover
• Copyright: 2005-11-14
• Publisher: Chapman & Hall/

Summary

Considered highly exotic tools as recently as the late 1990s, microarrays are now ubiquitous in biological research. Traditional statistical approaches to design and analysis were not developed to handle the high-dimensional, small sample problems posed by microarrays. In just a few short years the number of statistical papers providing approaches to analyzing microarray data has gone from almost none to hundreds if not thousands. This overwhelming deluge is quite daunting to either the applied investigator looking for methodologies or the methodologist trying to keep up with the field. DNA Microarrays and Related Genomics Techniques: Design, Analysis, and Interpretation of Experimentsconsolidates discussions of methodological advances into a single volume. The book "s structure parallels the steps an investigator or an analyst takes when conducting and analyzing a microarray experiment from conception to interpretation. It begins with foundational issues such as ensuring the quality and integrity of the data and assessing the validity of the statistical models employed, then moves on to cover critical aspects of designing a microarray experiment. The book includes discussions of power and sample size, where only very recently have developments allowed such calculations in a high dimensional context, followed by several chapters covering the analysis of microarray data. The amount of space devoted to this topic reflects both the variety of topics and the effort investigators have devoted to developing new methodologies. In closing, the book explores the intellectual frontier “ interpretation of microarray data. It discusses new methods for facilitating and affecting formalization of the interpretation process and the movement to make large high dimensional datasets public for further analysis, and methods for doing so. There is no question that this field will continue to advance rapidly and some of the specific methodologies discussed in this book will be replaced by new advances. Nevertheless, the field is now at a point where a foundation of key categories of methods has been laid out and begun to settle. Although the details may change, the majority of the principles described in this book and the foundational categories it contains will stand the test of time, making the book a touchstone for researchers in this field.

Table of Contents

Microarray Platforms	1	(8)
Patrick M. Gaffney
Kathy L. Moser
Normalization of Microarray Data	9	(20)
Rudolph S. Parrish
Robert R. Delongchamp
Microarray Quality Control and Assessment	29	(28)
David Finkelstein
Michael Janis
Alan Williams
Kathryn Steiger
Jacques Retief
Epistemological Foundations of Statistical Methods for High-Dimensional Biology	57	(20)
Stanislav O. Zakharkin
Tapan Mehta
Murat Tanik
David B. Allison
The Role of Sample Size on Measures of Uncertainty and Power	77	(18)
Gary L. Gadbury
Qinfang Xiang
Jode W. Edwards
Grier P. Page
David B. Allison
Pooling Biological Samples in Microarray Experiments	95	(16)
Christina M. Kendziorski
Designing Microarrays for the Analysis of Gene Expressions	111	(20)
Jane Y. Chang
Jason C. Hsu
Overview of Standard Clustering Approaches for Gene Microarray Data Analysis	131	(28)
Elizabeth Garrett-Mayer
Cluster Stability	159	(18)
Bernard S. Gorman
Kui Zhang
Dimensionality Reduction and Discrimination	177	(20)
Jeanne Kowalski
Zhen Zhang
Modeling Affymetrix Data at the Probe Level	197	(26)
Tzu-Ming Chu
Shibing Deng
Russell D. Wolfinger
Parametric Linear Models	223	(22)
Christopher S. Coffey
Stacey S. Cofield
The Use of Nonparametric Procedures in the Statistical Analysis of Microarray Data	245	(22)
T. Mark Beasley
Jacob P.L. Brand
Jeffrey D. Long
Bayesian Analysis of Microarray Data	267	(22)
Jode W. Edwards
Pulak Ghosh
False Discovery Rate and Multiple Comparison Procedures	289	(16)
Chiara Sabatti
Using Standards to Facilitate Interoperation of Heterogeneous Microarray Databases and Analytic Tools	305	(16)
Kei-Hoi Cheung
Postanalysis Interpretation: ``What Do I Do with This Gene List?''	321	(14)
Michael V. Osier
Combining High Dimensional Biological Data to Study Complex Diseases and Quantitative Traits	335	(26)
Grier P. Page
Douglas M. Ruden
Index	361