Design and analysis of DNA microarray investigations:
Saved in:
| Format: | Book |
|---|---|
| Language: | English |
| Published: |
New York, NY [u.a.]
Springer
2003
|
| Series: | Statistics for biology and health
|
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Item Description: | Literaturverz. S. 185 - 194 |
| Physical Description: | X, 199 S. Ill., graph. Darst. |
| ISBN: | 0387001352 |
Staff View
MARC
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Record in the Search Index
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| adam_text | Contents
Acknowledgments v
1 Introduction 1
2 DNA Microarray Technology 5
2.1 Overview 5
2.2 Measuring Label Intensity 5
2.3 Labeling Methods 6
2.4 Printed Microarrays 7
2.5 Affymetrix GeneChip™ Arrays 9
2.6 Other Microarray Platforms 10
3 Design of DNA Microarray Experiments 11
3.1 Introduction 11
3.2 Study Objectives 12
3.2.1 Class Comparison 12
3.2.2 Class Prediction 13
3.2.3 Class Discovery 13
3.2.4 Pathway Analysis 13
3.3 Comparing Two RNA Samples 13
3.4 Sources of Variation and Levels of Replication 14
3.5 Pooling of Samples 16
3.6 Pairing Samples on Dual Label Microarrays 17
3.6.1 The Reference Design 17
3.6.2 The Balanced Block Design 19
3.6.3 The Loop Design 20
3.7 Reverse Labeling (Dye Swap) 21
3.8 Number of Biological Replicates Needed 23
x Contents
9.3 Graphical Displays 125
9.3.1 Classical Multidimensional Scaling 125
9.3.2 Nonmetric Multidimensional Scaling 131
9.4 Clustering Algorithms 131
9.4.1 Hierarchical Clustering 13j
9.4.2 A; Means Clustering 13§
9.4.3 Self Organizing Maps 142
9.4.4 Other Clustering Procedures 145
9.5 Assessing the Validity of Clusters 146
9.5.1 Global Tests of Clustering ...148
9.5.2 Estimating the Number of Clusters 150
9.5.3 Assessing Reproduciblity of Individual Clusters 152
A Basic Biology of Gene Expression 157
A.I Introduction 165
B Description of Gene Expression Datasets Used
as Examples 165
B.I Introduction 165
B.2 Bittner Melanoma Data 165
B.3 Luo Prostate Data 166
B.4 Perou Breast Data 166
B.5 Tamayo HL 60 Data 167
B.6 Hedenfalk Breast Cancer Data 168
C BRB ArrayTools 169
C.I Software Description 169
C.2 Analysis of Bittner Melanoma Data 171
C.3 Analysis of Perou Breast Cancer Chemotherapy Data 178
0.4 Analysis of Hedenfalk Breast Cancer Data 182
References 185
Index 195
|
| adam_txt |
Contents
Acknowledgments v
1 Introduction 1
2 DNA Microarray Technology 5
2.1 Overview 5
2.2 Measuring Label Intensity 5
2.3 Labeling Methods 6
2.4 Printed Microarrays 7
2.5 Affymetrix GeneChip™ Arrays 9
2.6 Other Microarray Platforms 10
3 Design of DNA Microarray Experiments 11
3.1 Introduction 11
3.2 Study Objectives 12
3.2.1 Class Comparison 12
3.2.2 Class Prediction 13
3.2.3 Class Discovery 13
3.2.4 Pathway Analysis 13
3.3 Comparing Two RNA Samples 13
3.4 Sources of Variation and Levels of Replication 14
3.5 Pooling of Samples 16
3.6 Pairing Samples on Dual Label Microarrays 17
3.6.1 The Reference Design 17
3.6.2 The Balanced Block Design 19
3.6.3 The Loop Design 20
3.7 Reverse Labeling (Dye Swap) 21
3.8 Number of Biological Replicates Needed 23
x Contents
9.3 Graphical Displays 125
9.3.1 Classical Multidimensional Scaling 125
9.3.2 Nonmetric Multidimensional Scaling 131
9.4 Clustering Algorithms 131
9.4.1 Hierarchical Clustering 13j
9.4.2 A; Means Clustering 13§
9.4.3 Self Organizing Maps 142
9.4.4 Other Clustering Procedures 145
9.5 Assessing the Validity of Clusters 146
9.5.1 Global Tests of Clustering .148
9.5.2 Estimating the Number of Clusters 150
9.5.3 Assessing Reproduciblity of Individual Clusters 152
A Basic Biology of Gene Expression 157
A.I Introduction 165
B Description of Gene Expression Datasets Used
as Examples 165
B.I Introduction 165
B.2 Bittner Melanoma Data 165
B.3 Luo Prostate Data 166
B.4 Perou Breast Data 166
B.5 Tamayo HL 60 Data 167
B.6 Hedenfalk Breast Cancer Data 168
C BRB ArrayTools 169
C.I Software Description 169
C.2 Analysis of Bittner Melanoma Data 171
C.3 Analysis of Perou Breast Cancer Chemotherapy Data 178
0.4 Analysis of Hedenfalk Breast Cancer Data 182
References 185
Index 195 |
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| institution | BVB |
| isbn | 0387001352 |
| language | English |
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| spelling | Design and analysis of DNA microarray investigations Richard M. Simon ... New York, NY [u.a.] Springer 2003 X, 199 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Statistics for biology and health Literaturverz. S. 185 - 194 Biologia larpcal Estatística aplicada larpcal DNA microarrays Statistical methods Data Interpretation, Statistical Oligonucleotide Array Sequence Analysis methods Research Design Statistik (DE-588)4056995-0 gnd rswk-swf DNS (DE-588)4070512-2 gnd rswk-swf Microarray (DE-588)4544227-7 gnd rswk-swf DNS (DE-588)4070512-2 s Microarray (DE-588)4544227-7 s Statistik (DE-588)4056995-0 s DE-604 Simon, Richard M. 1943- Sonstige (DE-588)128738170 oth HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=015656270&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Design and analysis of DNA microarray investigations Biologia larpcal Estatística aplicada larpcal DNA microarrays Statistical methods Data Interpretation, Statistical Oligonucleotide Array Sequence Analysis methods Research Design Statistik (DE-588)4056995-0 gnd DNS (DE-588)4070512-2 gnd Microarray (DE-588)4544227-7 gnd |
| subject_GND | (DE-588)4056995-0 (DE-588)4070512-2 (DE-588)4544227-7 |
| title | Design and analysis of DNA microarray investigations |
| title_auth | Design and analysis of DNA microarray investigations |
| title_exact_search | Design and analysis of DNA microarray investigations |
| title_exact_search_txtP | Design and analysis of DNA microarray investigations |
| title_full | Design and analysis of DNA microarray investigations Richard M. Simon ... |
| title_fullStr | Design and analysis of DNA microarray investigations Richard M. Simon ... |
| title_full_unstemmed | Design and analysis of DNA microarray investigations Richard M. Simon ... |
| title_short | Design and analysis of DNA microarray investigations |
| title_sort | design and analysis of dna microarray investigations |
| topic | Biologia larpcal Estatística aplicada larpcal DNA microarrays Statistical methods Data Interpretation, Statistical Oligonucleotide Array Sequence Analysis methods Research Design Statistik (DE-588)4056995-0 gnd DNS (DE-588)4070512-2 gnd Microarray (DE-588)4544227-7 gnd |
| topic_facet | Biologia Estatística aplicada DNA microarrays Statistical methods Data Interpretation, Statistical Oligonucleotide Array Sequence Analysis methods Research Design Statistik DNS Microarray |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=015656270&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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