Bioconductor Case StudiesBioconductor software has become a standard tool for the analysis and comprehension of data from high-throughput genomics experiments. Its application spans a broad field of technologies used in contemporary molecular biology. In this volume, the authors present a collection of cases to apply Bioconductor tools in the analysis of microarray gene expression data. Topics covered include * import and preprocessing of data from various sources * statistical modeling of differential gene expression * biological metadata * application of graphs and graph rendering * machine learning for clustering and classification problems * gene set enrichment analysis Each chapter of this book describes an analysis of real data using hands-on example driven approaches. Short exercises help in the learning process and invite more advanced considerations of key topics. The book is a dynamic document. All the code shown can be executed on a local computer, and readers are able to reproduce every computation, figure, and table. |
Contents
1 | |
5 | |
3 Processing AffymetrixExpression Data | 25 |
4 TwoColor Arrays | 46 |
5 FoldChanges LogRatios Background Correction Shrinkage Estimation and Variance Stabilization | 63 |
6 Easy Differential Expression | 83 |
7 Differential Expression | 89 |
8 Annotation and Metadata | 103 |
10 Unsupervised Machine Learning | 137 |
11 Using Graphs for Interactome Data | 159 |
12 Graph Layout | 173 |
13 Gene Set Enrichment Analysis | 192 |
14 Hypergeometric Testing Used for Gene Set Enrichment Analysis | 207 |
15 Solutions to Exercises | 221 |
270 | |
277 | |
Other editions - View all
Bioconductor Case Studies Florian Hahne,Wolfgang Huber,Robert Gentleman,Seth Falcon Limited preview - 2010 |
Bioconductor Case Studies Florian Hahne,Wolfgang Huber,Robert Gentleman,Seth Falcon No preview available - 2008 |