Methods of microarray data analysis III : papers from CAMDA'02

Contributing Authors Preface Introduction SECTION I TUTORIALS THE BIOLOGY BEHIND GENE EXPRESSION: A BASIC TUTORIAL MICHAEL F. OCHS AND ERICA A. GOLEMIS MONITORING THE QUALITY OF MICROARRAY EXPERIMENTS KEVIN R. COOMBES, JINGWANG, LYNNE V. ABRUZZO OUTLIERS IN MICROARRAY DATA ANALYSIS RONALD K. PEARSON, GREGORY E. GONYE, AND JAMES S. SCHWABER SECTION II BEST PRESENTATION AWARD ORGAN-SPECIFIC DIFFERENCES IN GENE EXPRESSION AND UNIGENE ANNOTATIONS DESCRIBING SOURCE MATERIAL DAVID N. STIVERS, JINGWANG, GARY L. ROSNER, AND KEVIN R. COOMBES SECTION III ANALYZING IMAGES ix xi 1 7 9 25 41 57 59 73 vi Methods of Microarray Data Analysis III CHARACTERIZATION, MODELING, AND SIMULATION OF MOUSE MICROARRAY DATA DAVID S. LALUSH TOPOLOGICAL ADJUSTMENTS TO GENECHIP EXPRESSION VALUES ANDREY PTITSYN SECTION IV NORMALIZING RAW DATA COMPARISON OF NORMALIZATION METHODS FOR CDNA MICROARRAYS LILINGWARREN, BEN LIU SECTION V CHARACTERIZING TECHNICAL AND BIOLOGICAL VARIANCE SIMULTANEOUS ASSESSMENT OF TRANSCRIPTOMIC VARIABILITY AND TISSUE EFFECTS IN THE NORMAL MOUSE SHIBING DENG, TZU-MING CHU, AND RUSSWOLFINGER HOW MANY MICE AND HOW MANY ARRAYS? REPLICATION IN MOUSE CDNA MICROARRAY EXPERIMENTS XIANGQIN CUI AND GARY A. CHURCHILL BAYESIAN CHARACTERIZATION OF NATURAL VARIATION IN GENE EXPRESSION MADHUCHHANDA BHATTACHARJEE, COLIN PRITCHARD, MIKKO J. SlLLANPÄÄ AND ELJA ARJAS SECTION VI INVESTIGATING CROSS HYBRIDIZATION ON OLIGONUCLEOTIDE MICROARRAYS QUANTIFICATION OF CROSS HYBRIDIZATION ON OLIGONUCLEOTIDE MICROARRAYS LI ZHANG, KEVIN R. COOMBES, LIANCHUN XIAO ASSESSING THE POTENTIAL EFFECT OF CROSS-HYBRIDIZATION ON OLIGONUCLEOTIDE MICROARRAYS SEMAN KACHALO, ZAREMA ARBIEVA AND JIE LIANG WHO ARE THOSE STRANGERS IN THE LATIN SQUARE? WEN-PING HSIEH, TZU-MING CHU, AND RUSSWOLFINGER 75 93 103 105 123 125 139 155 173 175 185 199 Methods of Microarray Data Analysis III vii SECTION VII FINDING PATTERNS AND SEEKING BIOLOGICAL EXPLANATIONS BAYESIAN DECOMPOSITION CLASSIFICATION OF THE PROJECT NORMAL DATA SET 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 RAMÓN DÍAZ-URIARTE, FÁTIMA AL-SHAHROUR, AND JOAQUÍN DOPAZO Acknowledgments Index 209 211 233 249 251