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Robert Gentleman, Vincent J. Carey, Wolfgang Huber, Rafael A. Irizarry and Sandrine Dudoit
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Front matter
3-109
Part I / Preprocessing data from genomic experiments
3-12
Preprocessing Overview
13-32
Preprocessing High-density Oligonucleotide Arrays
33-47
Quality Assessment of Affymetrix GeneChip Data
49-69
Preprocessing Two-Color Spotted Arrays
71-90
Cell-Based Assays
91-109
SELDI-TOF Mass Spectrometry Protein Data
113-179
Part II / Meta-data: biological annotation and visualization
113-133
Meta-data Resources and Tools in Bioconductor
135-146
Querying On-line Resources
147-160
Interactive Outputs
161-179
Visualizing Data
183-326
Part III / Statistical analysis for genomic experiments
183-187
Analysis Overview
189-208
Distance Measures in DNA Microarray Data Analysis
209-228
Cluster Analysis of Genomic Data
229-248
Analysis of Differential Gene Expression Studies
249-271
Multiple Testing Procedures: the multtest Package and Applications to Genomics
273-292
Machine Learning Concepts and Tools for Statistical Genomics
293-311
Ensemble Methods of Computational Inference
313-326
Browser-based Affymetrix Analysis and Annotation
329-394
Part IV / Graphs and networks
329-336
Introduction and Motivating Examples
337-346
Graphs
347-368
Bioconductor Software for Graphs
369-394
Case Studies Using Graphs on Biological Data
397-442
Part V / Case studies
397-420
limma: Linear Models for Microarray Data
421-430
Classification with Gene Expression Data
431-442
From CEL Files to Annotated Lists of Interesting Genes
443-473
Back matter
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