Exploration and analysis of DNA microarray and protein array data:
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| Main Authors: | , |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Hoboken, NJ
Wiley
2004
|
| Series: | Wiley series in probability and statistics
|
| Subjects: | |
| Online Access: | Publisher description Table of contents Inhaltsverzeichnis |
| Item Description: | Includes bibliographical references and index |
| Physical Description: | XIV, 246 S. |
| ISBN: | 0471273988 |
Staff View
MARC
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| 100 | 1 | |a Amaratunga, Dhammika |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a Exploration and analysis of DNA microarray and protein array data |c Dhammika Amaratunga, Javier Cabrera |
| 264 | 1 | |a Hoboken, NJ |b Wiley |c 2004 | |
| 300 | |a XIV, 246 S. | ||
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| 490 | 0 | |a Wiley series in probability and statistics | |
| 500 | |a Includes bibliographical references and index | ||
| 650 | 7 | |a Biologia molecular |2 larpcal | |
| 650 | 7 | |a DNA Microarrays |2 gtt | |
| 650 | 7 | |a Dna (métodos estatísticos) |2 larpcal | |
| 650 | 4 | |a DNA microarrays |x Statistical methods | |
| 650 | 4 | |a Oligonucleotide Array Sequence Analysis |x statistics & numerical data | |
| 650 | 4 | |a Protein Array Analysis |x statistics & numerical data | |
| 650 | 4 | |a Protein microarrays |x Statistical methods | |
| 700 | 1 | |a Cabrera, Javier |e Verfasser |4 aut | |
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Record in the Search Index
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| adam_text | Exploration and Analysis
of DNA Microarray and
Protein Array Data
DHAMMIKA AMARATUNGA
Johnson amp; Johnson Pharmaceutical R amp;D
Raritan, NJ
JAVIER CABRERA
Rutgers University
Piscataway, NJ
WILEY-
MNTERSCIENCE
A JOHN WILEY amp; SONS, INC , PUBLICATION
Contents
Preface xiii
1 A Brief Introduction 1
11A Note on Exploratory Data Analysis, 3
1 2 Computing Considerations and Software, 4
13A Brief Outline of the Book, 5
2 Genomics Basics 8
2 1 Genes, 8
2 2 DNA, 9
2 3 Gene Expression, 10
2 4 Hybridization Assays and Other Laboratory
Techniques, 12
2 5 The Human Genome, 14
2 6 Genome Variations and Their Consequences, 15
2 7 Genomics, 17
2 8 The Role of Genomics in Pharmaceutical Research 18
2 9 Proteins, 20
2 10 Bioinformatics, 21
Supplementary Reading, 22
Exercises, 22
3 Microarrays 23
3 1 Types of Microarray Experiments, 24
311 Experiment Type 1: Tissue-Specific Gene
Expression, 24
312 Experiment Type 2: Developmental Genetics, 24
vii
Vlll CONTENTS
313 Experiment Type 3: Genetic Diseases, 25
314 Experiment Type 4: Complex Diseases, 26
315 Experiment Type 5: Pharmacological Agents, 26
316 Experiment Type 6: Plant Breeding, 27
317 Experiment Type 7: Environmental
Monitoring, 27
32A Very Simple Hypothetical Microarray Experiment, 28
33A Typical Microarray Experiment, 30
331 Microarray Preparation, 30
332 Sample Preparation, 32
333 The Hybridization Step, 32
334 Scanning the Microarray, 33
335 Interpreting the Scanned Image, 33
3 4 Multichannel cDNA Microarrays, 34
3 5 Oligonucleotide Arrays, 35
3 6 Bead-Based Arrays, 36
3 7 Confirmation of Microarray Results, 37
Supplementary Reading and Electronic References, 37
Exercises, 37
4 Processing the Scanned Image 39
4 1 Converting the Scanned Image to the Spotted Image, 39
411 Gridding, 40
412 Segmentation, 40
413 Quantification, 41
4 2 Quality Assessment, 42
421 Visualizing the Spotted Image, 43
422 Numerical Evaluation of Array Quality, 44
423 Spatial Problems, 45
424 Spatial Randomness, 46
425 Quality Control of Arrays, 47
426 Assessment of Spot Quality, 48
4 3 Adjusting for Background, 49
431 Estimating the Background, 50
432 Adjusting for the Estimated Background, 53
4 4 Expression Level Calculation for Two-Channel cDNA
Microarrays, 53
4 5 Expression Level Calculation for Oligonucleotide
Arrays, 54
CONTENTS IX
451 The Average Difference, 54
452A Weighted Average Difference, 54
453 Perfect Matches Only, 55
454 Background Adjustment Approach, 56
455 Model-Based Approach, 56
456 Absent-Present Calls, 56
Supplementary Reading, 58
Exercises, 58
5 Preprocessing Microarray Data 60
5 1 Logarithmic Transformation, 60
5 2 Variance Stabilizing Transformations, 62
5 3 Sources of Bias, 63
5 4 Normalization, 63
5 5 Intensity-Dependent Normalization, 65
551 Smooth Function Normalization, 68
552 Quantile Normalization, 68
553 Normalization of Oligonucleotide Arrays, 70
554 Normalization of Two-Channel Arrays, 70
555 Spatial Normalization, 71
556 Stagewise Normalization, 72
5 6 Judging the Success of a Normalization, 73
5 7 Outlier Identification, 77
571 Nonresistant Rules for Outlier Identification, 77
572 Resistant Rules for Outlier Identification, 78
5 8 Assessing Replicate Array Quality, 79
Exercises, 80
6 Summarization 82
6 1 Replication, 82
6 2 Technical Replicates, 83
6 3 Biological Replicates, 86
6 4 Experiments with Both Technical and Biological
Replicates, 87
6 5 Multiple Oligonucleotide Arrays, 90
6 6 Estimating Fold Change in Two-Channel Experiments, 92
6 7 Bayes Estimation of Fold Change, 93
Exercises, 94
X CONTENTS
7 Two-Group Comparative Experiments 95
7 1 Basics of Statistical Hypothesis Testing, 96
7 2 Fold Changes, 99
7 3 The Two-Sample t Test, 100
7 4 Diagnostic Checks, 103
7 5 Robust / Tests, 104
7 6 Randomization Tests, 105
7 7 The Mann-Whitney-Wilcoxon Rank Sum Test, 108
7 8 Multiplicity, 109
781A Pragmatic Approach to the Issue of
Multiplicity, 109
782 Simple Multiplicity Adjustments, 110
783 Sequential Multiplicity Adjustments, 111
7 9 The False Discovery Rate, 113
791 The Positive False Discovery Rate, 114
7 10 Small Variance-Adjusted t Tests and SAM, 115
7 10 1 Modifying the / Statistic, 117
7 10 2 Assesing Significance with the SAM t Statistic, 117
7 10 3 Strategies for Using SAM, 120
7 10 4 An Empirical Bayes Framework, 120
7 10 5 Understanding the SAM Adjustment, 121
7 11 Conditional t, 123
7 12 Borrowing Strength across Genes, 126
7 12 1 Simple Methods, 127
7 12 2 A Bayesian Model, 129
7 13 Two-Channel Experiments, 130
7 13 1 The Paired Sample t Test and SAM, 131
7 13 2 Borrowing Strength via Hierarchical
Modeling, 131
Supplementary Reading, 133
Exercises, 133
8 Model-Based Inference and Experimental Design Considerations 135
8 1 The/Test, 136
8 2 The Basic Linear Model, 138
8 3 Fitting the Model in Two Stages, 140
8 4 Multichannel Experiments, 141
8 5 Experimental Design Considerations, 141
CONTENTS Xi
851 Comparing Two Varieties with Two-Channel
Microarrays, 141
852 Comparing Multiple Varieties with Two-Channel
Microarrays, 143
853 Single-Channel Microarray Experiments, 145
8 6 Miscellaneous Issues, 146
Supplementary Reading, 147
Exercises, 147
9 Pattern Discovery 149
9 1 Initial Considerations, 149
Cluster
Seeking
Analysis, 151
Dissimilarity Measures and Similarity
Measures, 152
Guilt by Association, 155
Hierarchical Clustering, 155
Partitioning Methods, 160
Model-Based Clustering, 166
Chinese Restaurant Clustering, 167
Discussion, 168
; Patterns Visually, 168
Principal Components Analysis, 169
Factor Analysis, 174
Biplots, 176
Spectral Map Analysis, 177
Multidimensional Scaling, 179
Projection Pursuit, 179
Data Visualization with the Grand Tour and
Projection Pursuit, 181
Two-Way Clustering, 182
Block Clustering, 182
Gene Shaving, 182
The Plaid Model, 183
Software Notes, 184
Supplementary Reading, 184
Exercises, 185
10 Class Prediction 186
10 1 Initial Considerations, 187
XII CONTENTS
10 1 1 Misclassification Rates, 188
10 1 2 Reducing the Number of Classifiers, 189
10 2 Linear Discriminant Analysis, 193
10 3 Extensions of Fisher s LDA, 197
10 4 Nearest Neighbors, 200
10 5 Recursive Partitioning, 201
10 5 1 Classification Trees, 201
10 5 2 Activity Region Finding, 206
10 6 Neural Networks, 206
10 7 Support Vector Machines, 208
10 8 Integration of Genomic Information, 210
10 8 1 Integration of Gene Expression Data and
Molecular Structure Data, 210
10 8 2 Pathway Inference, 211
Software Notes, 211
Supplementary Reading, 212
Exercises, 212
11 Protein Arrays 214
11 1 Introduction, 214
11 2 Protein Array Experiments, 215
11 3 Special Issues with Protein Arrays, 216
11 4 Analysis, 217
11 5 Using Antibody Antigen Arrays to Measure Protein
Concentrations, 218
Exercises, 221
References 222
Author Index 237
Subject Index 241
|
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| id | DE-604.BV017109796 |
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| indexdate | 2024-07-09T19:13:50Z |
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| language | English |
| lccn | 2003050097 |
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| spelling | Amaratunga, Dhammika Verfasser aut Exploration and analysis of DNA microarray and protein array data Dhammika Amaratunga, Javier Cabrera Hoboken, NJ Wiley 2004 XIV, 246 S. txt rdacontent n rdamedia nc rdacarrier Wiley series in probability and statistics Includes bibliographical references and index Biologia molecular larpcal DNA Microarrays gtt Dna (métodos estatísticos) larpcal DNA microarrays Statistical methods Oligonucleotide Array Sequence Analysis statistics & numerical data Protein Array Analysis statistics & numerical data Protein microarrays Statistical methods Cabrera, Javier Verfasser aut http://www.loc.gov/catdir/description/wiley038/2003050097.html Publisher description http://www.loc.gov/catdir/toc/wiley032/2003050097.html Table of contents HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=010317120&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Amaratunga, Dhammika Cabrera, Javier Exploration and analysis of DNA microarray and protein array data Biologia molecular larpcal DNA Microarrays gtt Dna (métodos estatísticos) larpcal DNA microarrays Statistical methods Oligonucleotide Array Sequence Analysis statistics & numerical data Protein Array Analysis statistics & numerical data Protein microarrays Statistical methods |
| title | Exploration and analysis of DNA microarray and protein array data |
| title_auth | Exploration and analysis of DNA microarray and protein array data |
| title_exact_search | Exploration and analysis of DNA microarray and protein array data |
| title_full | Exploration and analysis of DNA microarray and protein array data Dhammika Amaratunga, Javier Cabrera |
| title_fullStr | Exploration and analysis of DNA microarray and protein array data Dhammika Amaratunga, Javier Cabrera |
| title_full_unstemmed | Exploration and analysis of DNA microarray and protein array data Dhammika Amaratunga, Javier Cabrera |
| title_short | Exploration and analysis of DNA microarray and protein array data |
| title_sort | exploration and analysis of dna microarray and protein array data |
| topic | Biologia molecular larpcal DNA Microarrays gtt Dna (métodos estatísticos) larpcal DNA microarrays Statistical methods Oligonucleotide Array Sequence Analysis statistics & numerical data Protein Array Analysis statistics & numerical data Protein microarrays Statistical methods |
| topic_facet | Biologia molecular DNA Microarrays Dna (métodos estatísticos) DNA microarrays Statistical methods Oligonucleotide Array Sequence Analysis statistics & numerical data Protein Array Analysis statistics & numerical data Protein microarrays Statistical methods |
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