2008

Bioconductor Case Studies

Authors:

ISBN: 978-0-387-77239-4 (Print) 978-0-387-77240-0 (Online)

Table of contents (15 chapters)

  1. Front Matter

    Pages I-XI

  2. No Access

    Book Chapter

    Pages 1-4

    The ALL Dataset

  3. No Access

    Book Chapter

    Pages 5-24

    R and Bioconductor Introduction

  4. No Access

    Book Chapter

    Pages 25-45

    Processing Affymetrix Expression Data

  5. No Access

    Book Chapter

    Pages 47-61

    Two Color Arrays

  6. No Access

    Book Chapter

    Pages 63-82

    Fold Changes, Log Ratios, Background Correction, Shrinkage Estimation, and Variance Stabilization

  7. No Access

    Book Chapter

    Pages 83-88

    Easy Differential Expression

  8. No Access

    Book Chapter

    Pages 89-102

    Differential Expression

  9. No Access

    Book Chapter

    Pages 103-119

    Annotation and Metadata

  10. No Access

    Book Chapter

    Pages 121-136

    Supervised Machine Learning

  11. No Access

    Book Chapter

    Pages 137-157

    Unsupervised Machine Learning

  12. No Access

    Book Chapter

    Pages 159-172

    Using Graphs for Interactome Data

  13. No Access

    Book Chapter

    Pages 173-191

    Graph Layout

  14. No Access

    Book Chapter

    Pages 193-205

    Gene Set Enrichment Analysis

  15. No Access

    Book Chapter

    Pages 207-220

    Hypergeometric Testing Used for Gene Set Enrichment Analysis

  16. No Access

    Book Chapter

    Pages 221-269

    Solutions to Exercises

  17. Back Matter

    Pages 271-283