Microarray technology in practice:
Saved in:
| Main Authors: | , , |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Amsterdam [u.a.]
Elsevier, Acad. Press
2009
|
| Edition: | 1. ed. |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | X, 449 S. Ill., graph. Darst. |
| ISBN: | 9780123725165 012372516X |
Staff View
MARC
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| 100 | 1 | |a Russell, Steve |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a Microarray technology in practice |c Steve Russell, Lisa A. Meadows and Roslin R. Russell |
| 250 | |a 1. ed. | ||
| 264 | 1 | |a Amsterdam [u.a.] |b Elsevier, Acad. Press |c 2009 | |
| 300 | |a X, 449 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 650 | 4 | |a DNA microarrays | |
| 650 | 4 | |a Oligonucleotide Array Sequence Analysis | |
| 650 | 0 | 7 | |a Microarray |0 (DE-588)4544227-7 |2 gnd |9 rswk-swf |
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| 700 | 1 | |a Meadows, Lisa A. |e Verfasser |4 aut | |
| 700 | 1 | |a Russell, Roslin R. |e Verfasser |4 aut | |
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| 999 | |a oai:aleph.bib-bvb.de:BVB01-017153051 | ||
Record in the Search Index
| _version_ | 1804138668586172416 |
|---|---|
| adam_text | Contents
Foreword and acknowledgments
ix
1.
Introduction
1.1.
Technology
і
1.2.
A Brief History
4
1.3.
A Brief Outline
9
References
13
2
The Basics of Experimental Design
2.1.
Sources of Variation in Microarray Gene
Expression Measurements
18
2.2.
Controls and Replicates
21
2.3.
Experimental Designs
26
2.4.
Summary
32
References
32
3
Designing and Producing Microarrays
3.1.
Probe Selection
36
3.2.
cDNA and Amplicon Probes
39
3.3.
Oligonucleotide Probes
40
3.4.
Preparing Arrays
55
3.5.
Summary
65
References
65
4
Sample Collection and Labeling
4.1.
Sample Collection and
RNA
Extraction
72
4.2.
RNA
Quality Assessment
73
4.3.
cDNA Production
76
4.4.
Labeling Methods
78
4.5.
Signal Amplification
84
vi
Contents
4.6.
RNA
Amplification
86
4.7.
Amplification Methods Compared
95
4.8.
Quality Control for Fluorescently Labeled Samples
97
4.9.
Summary
97
References
98
5
Hybridization and Scanning
5.1.
Hybridization
102
5.2.
Data Acquisition
106
5.3.
Finding Spots
115
5.4.
Method Comparison
121
5.5.
Data Extraction
122
5.6.
Quality Control Basics
127
5.7.
Summary
129
References
130
6
Data Preprocessing
6.1.
Preprocessing Rationale
136
6.2.
Sources of Systematic Error
138
6.3.
Background Correction
139
6.4.
Data Filtering, Flagging and Weighting
141
6.5.
Treating Missing Values
142
6.6.
Data Transformation
145
6.7.
Dealing with Spatial Effects
158
6.8.
Print-Tip Group Loess Normalization
161
6.9.
Two-Dimensional (2D) Loess
163
6.10.
Composite Loess Normalization
163
6.11.
Weighted Loess Normalization
165
6.12.
Probe Replicates Used for Effective Normalization
166
6.13.
Between-Array Normalization
167
6.14.
Other Quality Control Considerations
171
6.15.
MicroArray
Quality Control Consortium (MAQC)
172
6.16.
The External
RNA
Controls Consortium (ERCC)
172
6.17.
The EMERALD Consortium
173
6.18.
Preprocessing Affymetrix
Genechip Data 173
6.19.
Probe Correction and Summarization
178
6.20.
Background Correction
180
6.21.
Normalization
184
6.22.
Summary
185
References
186
7
Differential Expression
7.1.
Introduction
191
7.2.
Statistical Inference
195
7.3.
Parametric Statistics
208
Contents
vii
7.4. Linear Models
for
Microarray Data
(LIMMA)
221
7.5. Nonparametric
Statistics
239
7.6.
Gene-Class Testing
246
7.7.
Summary
257
References
261
8
Clustering and Classification
8.1.
Introduction
272
8.2.
Similarity Metrics
274
8.3.
Unsupervised Analysis Methods: Clustering and Partitioning
276
8.4.
Assessing Cluster Quality
287
8.5.
Dimensional Reduction
291
8.6.
Supervised Methods
295
8.7.
Assessing Model Quality
300
8.S. Summary
301
References
302
9
Microarray Data Repositories and Warehouses
9.1.
Introduction
307
9.2.
ArrayExpress
309
9.3.
Gene Expression Omnibus
(GEO)
313
9.4.
Other Repositories and Warehouses
322
9.5.
Summary
326
References
328
10
Beyond Expression Arrays: Genome Analysis
10.1.
Genome Arrays
334
10.2.
Exon Arrays
336
10.3.
Tiling Arrays
337
10.4.
Amplicon and
ВАС
Arrays
338
10.5.
Oligonucleotide Tiles
342
10.6.
Using Tiling Arrays
344
10.7.
Analysis of Tiling Arrays
354
10.8.
Summary
357
References
358
11
Medical Applications of Microarray Technology
11.1.
Introduction
364
11.2.
Investigating Pathogens: Malaria
367
1
1
.3.
Expression Profiling Human Disease
374
llAArray-CGH
381
11.5.
SNPs and Genotyping
390
11.6.
Summary
399
References
401
viii Contents
12
Other Array Technologies
12.1.
Protein-Binding Arrays
411
12.2.
Cell and Tissue Arrays
4
1
4
12.3.
Protein Arrays
418
12.4.
Summary
424
References
425
13
Future Prospects
13.1.
Arrays
431
13.2.
Labeling and Detection
433
13.3.
Imaging
434
13.4.
Analysis
436
References
437
Index
441
|
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| id | DE-604.BV035348875 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T21:31:51Z |
| institution | BVB |
| isbn | 9780123725165 012372516X |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-017153051 |
| oclc_num | 229025997 |
| open_access_boolean | |
| owner | DE-355 DE-BY-UBR DE-11 DE-860 |
| owner_facet | DE-355 DE-BY-UBR DE-11 DE-860 |
| physical | X, 449 S. Ill., graph. Darst. |
| publishDate | 2009 |
| publishDateSearch | 2009 |
| publishDateSort | 2009 |
| publisher | Elsevier, Acad. Press |
| record_format | marc |
| spelling | Russell, Steve Verfasser aut Microarray technology in practice Steve Russell, Lisa A. Meadows and Roslin R. Russell 1. ed. Amsterdam [u.a.] Elsevier, Acad. Press 2009 X, 449 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier DNA microarrays Oligonucleotide Array Sequence Analysis Microarray (DE-588)4544227-7 gnd rswk-swf Microarray (DE-588)4544227-7 s DE-604 Meadows, Lisa A. Verfasser aut Russell, Roslin R. Verfasser aut Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017153051&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Russell, Steve Meadows, Lisa A. Russell, Roslin R. Microarray technology in practice DNA microarrays Oligonucleotide Array Sequence Analysis Microarray (DE-588)4544227-7 gnd |
| subject_GND | (DE-588)4544227-7 |
| title | Microarray technology in practice |
| title_auth | Microarray technology in practice |
| title_exact_search | Microarray technology in practice |
| title_full | Microarray technology in practice Steve Russell, Lisa A. Meadows and Roslin R. Russell |
| title_fullStr | Microarray technology in practice Steve Russell, Lisa A. Meadows and Roslin R. Russell |
| title_full_unstemmed | Microarray technology in practice Steve Russell, Lisa A. Meadows and Roslin R. Russell |
| title_short | Microarray technology in practice |
| title_sort | microarray technology in practice |
| topic | DNA microarrays Oligonucleotide Array Sequence Analysis Microarray (DE-588)4544227-7 gnd |
| topic_facet | DNA microarrays Oligonucleotide Array Sequence Analysis Microarray |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017153051&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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