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  • Chapter 1
    The ALL Data Set
    • no figures
  • Chapter 2
    R and Bioconductor Introduction
    • Figure 2.1
    • Figure 2.2
    • Figure 2.3
  • Chapter 3
    Processing Affymetrix Expression Data
    • Figure 3.1
    • Figure 3.2
    • Figure 3.3
    • Figure 3.4
    • Figure 3.5
    • Figure 3.6
    • Figure 3.7
    • Figure 3.8
    • Figure 3.9
    • Figure 3.10
    • Figure 3.11
    • Figure 3.12
  • Chapter 4
    Two Color Arrays
    • Figure 4.1
    • Figure 4.2
    • Figure 4.3
    • Figure 4.4
    • Figure 4.5
    • Figure 4.6
    • Figure 4.7
  • Chapter 5
    Fold Changes, Log-ratios, Background Correction, Shrinkage Estimation and Variance Stabilisation
    • Figure 5.1
    • Figure 5.2
    • Figure 5.3
    • Figure 5.4
    • Figure 5.5
    • Figure 5.6
    • Figure 5.7
    • Figure 5.8
    • Figure 5.9
    • Figure 5.10
    • Figure 5.11
    • Figure 5.12
  • Chapter 6
    Easy Differential Expression
    • Figure 6.1
    • Figure 6.2
    • Figure 6.3
  • Chapter 7
    Differential Expression
    • Figure 7.1
    • Figure 7.2
    • Figure 7.3
    • Figure 7.4
    • Figure 7.5
    • Figure 7.6
    • Figure 7.7
    • Figure 7.8
  • Chapter 8
    Annotation and Metadata
    • Figure 8.1
    • Figure 8.2
    • Figure 8.3
    • Figure 8.4
    • Figure 8.5
  • Chapter 9
    Unsupervised Machine Learning
    • Figure 9.1
    • Figure 9.2
  • Chapter 10
    Supervised Machine Learning
    • Figure 10.1
    • Figure 10.2
    • Figure 10.3
    • Figure 10.4
    • Figure 10.5
    • Figure 10.6
    • Figure 10.7
    • Figure 10.8
  • Chapter 11
    Using Graphs for Interactome Data
    • Figure 11.1
    • Figure 11.2
    • Figure 11.3
  • Chapter 12
    Graph Layout
    • Figure 12.1
    • Figure 12.2
    • Figure 12.3
    • Figure 12.4
    • Figure 12.5
    • Figure 12.6
    • Figure 12.7
    • Figure 12.8
    • Figure 12.9
  • Chapter 13
    Gene Set Enrichment Analysis
    • Figure 13.1
    • Figure 13.2
    • Figure 13.3
  • Chapter 14
    Hypergeometric Testing used for Gene Set Enrichment Analysis
    • Figure 14.1