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Table Of Contents

Preface
List of Contributors
The ALL Dataset
1.1 Introduction
1.2 The ALL data
1.3 Data subsetting
1.4 Nonspecific filtering
2.3 Some basic R
2.4 Structures for genomic data
2.5 Graphics
Processing Affymetrix Expression Data
3.1 The input data: CEL files
3.2 Quality assessment
3.3 Preprocessing
3.4 Ranking and filtering probe sets
3.5 Advanced preprocessing
Two-Color Arrays
4.1 Introduction
4.2 Data import
4.3 Image plots
4.4 Normalization
4.5 Differential expression
5.1 Fold-changes and (log-)ratios
5.2 Background-correction and generalized logarithm
5.3 Calling VSN
5.4 How does VSN work?
5.6 Single-color normalization
5.7 The interpretation of glog-ratios
5.8 Reference normalization
Easy Differential Expression
6.1 Example data
6.2 Nonspecific filtering
7.1 Motivation
7.2 Nonspecific filtering
7.3 Differential expression
7.4 Multiple testing
7.5 Moderated test statistics and the limma package
7.7 When power increases
Annotation and Metadata
8.1 Our data
8.2 Multiple probe sets per gene
8.3 Categories and overrepresentation
8.4 Working with GO
8.5 Other annotations available
8.6 biomaRt
8.7 Database versions of annotation packages
Supervised Machine Learning
9.1 Introduction
9.2 The example dataset
9.3 Feature selection and standardization
9.4 Selecting a distance
9.5 Machine learning
9.6 Cross-validation
9.7 Random forests
9.8 Multigroup classification
Unsupervised Machine Learning
10.1 Preliminaries
10.2 Distances
10.3 How many clusters?
10.4 Hierarchical clustering
10.5 Partitioning methods
10.6 Self-organizing maps
10.7 Hopach
10.8 Silhouette plots
10.9 Exploring transformations
11.2 Exploring the protein interaction graph
11.3 The co-expression graph
11.5 Some harder problems
12.1 Introduction
12.2 Layout and rendering using Rgraphviz
12.3 Directed graphs
12.4 Subgraphs
12.5 Tooltips and hyperlinks on graphs
Gene Set Enrichment Analysis
13.1 Introduction
13.2 Data analysis
14.1 Introduction
14.2 The basic problem
14.3 Preprocessing and inputs
14.4 Outputs and result summarization
14.5 The conditional hypergeometric test
14.6 Other collections of gene sets
Solutions to Exercises
2 R and Bioconductor Introduction
3 Processing Affymetrix Expression Data
4 Two-Color Arrays
8 Annotation and Metadata
9 Supervised Machine Learning
10 Unsupervised Machine Learning
11 Using Graphs for Interactome Data
12 Graph Layout
13 Gene Set Enrichment Analysis
References
Index
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Bioconductor+Case+Studies+(Use+R!)

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Published by fukunaga_smc

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Categories:Topics, Art & Design
Published by: fukunaga_smc on Jan 15, 2011
Copyright:Attribution Non-commercial

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07/24/2013

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