Methods of Microarray Data Analysis III

by Johnson, Kimberly F.; Lin, Simon M.

• ISBN13: 9781402075827
• ISBN10: 1402075820
• Format: Hardcover
• Copyright: 2003-09-30
• Publisher: Kluwer Academic Pub

Summary

As microarray technology has matured, data analysis methods have advanced as well. Methods Of Microarray Data Analysis III is the third book in this pioneering series dedicated to the existing new field of microarrays. While initial techniques focused on classification exercises (volume I of this series), and later on pattern extraction (volume II of this series), this volume focuses on data quality issues. Problems such as background noise determination, analysis of variance, and errors in data handling are highlighted. Three tutorial papers are presented to assist with a basic understanding of underlying principles in microarray data analysis, and twelve new papers are highlighted analyzing the same CAMDA'02 datasets: the Project Normal data set or the Affymetrix Latin Square data set. A comparative study of these analytical methodologies brings to light problems, solutions and new ideas. This book is an excellent reference for academic and industrial researchers who want to keep abreast of the state of art of microarray data analysis.

Author Biography

Kimberly F. Johnson is Director of Duke Cancer Center Information Systems and Director of Duke Bioinformatics Shared Resource, Duke University Medical Center. Simon M. Lin is Manager of Duke Bioinformatics Shared Resource, Duke University Medical Center.

Table of Contents

Contributing Authors	ix
Preface	xi
Introduction	1	(6)
SECTION I TUTORIALS	7	(50)
THE BIOLOGY BEHIND GENE EXPRESSION: A BASIC TUTORIAL	9	(16)
MICHAEL F. OCHS AND ERICA A. GOLEMIS
MONITORING THE QUALITY OF MICROARRAY EXPERIMENTS	25	(16)
KEVIN R. COOMBES, JING WANG, LYNNE V. ABRUZZO
OUTLINERS IN MICROARRAY DATA ANALYSIS	41	(16)
RONALD K. PEARSON, GREGORY E. GONYE, AND JAMES S. SCHWABER
SECTION II BEST PRESENTATION A WARD	57	(16)
ORGAN-SPECIFIC DIFFERENCES IN GENE EXPRESSION AND UNIGENE ANNOTATIONS DESCRIBING SOURCE MATERIAL	59	(14)
DAVID N. STIVERS, JING WANG, GARY L. ROSNER, AND KEVIN R. COOMBES
SECTION III ANALYZING IMAGES	73	(30)
CHARACTERIZATION, MODELING, AND SIMULATION OF MOUSE MICROARRAY DATA	75	(18)
DAVID S. LALUSH
TOPOLOGICAL ADJUSTMENTS TO GENECHIP EXPRESSION VALUES	93	(10)
ANDREY PTITSYN
SECTION IV NORMALIZING RAW DATA	103	(20)
COMPARISON OF NORMALIZATION METHODS FOR CDNA MICROARRAYS	105	(18)
LILING WARREN, BEN LIU
SECTION V CHARACTERIZING TECHNICAL AND BIOLOGICAL VARIANCE	123	(50)
SIMULTANEOUS ASSESSMENT OF TRANSCRIPTOMIC VARIABILITY AND TISSUE EFFECTS IN THE NORMAL MOUSE	125	(14)
SHIBING DENG, TZU-MING CHU, AND RUSS WOLFINGER
HOW MANY MICE AND HOW MANY ARRAYS? REPLICATION IN MOUSE CDNA MICROARRAY EXPERIMENTS	139	(16)
XIANGQIN CUI AND GARY A. CHURCHILL
BAYESIAN CHARACTERIZATION OF NATURAL VARIATION IN GENE EXPRESSION	155	(18)
MADHUCHHANDA BHATTACHARJEE, COLIN PRITCHARD, MIKKO J. SILLANPÄÄ AND EUA MUAS
SECTION VI INVESTIGATING CROSS HYBRIDIZATION ON OLIGONUCLEOTIDE MICROARRAYS	173	(36)
QUANTIFICATION OF CROSS HYBRIDIZATION ON OLIGONUCLEOTIDE MICROARRAYS	175	(10)
LI ZHANG, KEVIN R. COOMBES, LIANCHUN XIAO
ASSESSING THE POTENTIAL EFFECT OF CROSS-HYBRIDIZATION ON OLIGONUCLEOTIDE MICROARRAYS	185	(14)
SEMAN KACHALO, ZAREMA ARBIEVA AND JIE LIANG
WHO ARE THOSE STRANGERS IN THE LATIN SQUARE?	199	(10)
WEN-PING HSIEH, TZU-MING CHU, AND RUSS WOLFINGER
SECTION VII FINDING PATTERNS AND SEEKING BIOLOGICAL EXPLANATIONS	209	(40)
BAYESIAN DECOMPOSITION CLASSIFICATION OF THE PROJECT NORMAL DATA SET	211	(22)
T.D. MOLOSHOK, D. DATTA, A.V. KOSSENKOV, M.F. OCHS
THE USE OF GO TERMS TO UNDERSTAND THE BIOLOGICAL SIGNIFICANCE OF MICROARRAY DIFFERENTIALGENE EXPRESSION DATA	233	(16)
RAMÓN DIAZ-URIARTE, FÁTIMA AL-SHAHROUR, AND JOAQUIN DOPAZO
Acknowledgments	249	(2)
Index	251