Bioconductor Case Studies

1. The ALL Dataset
F. Hahne, R. Gentleman

2. R and Bioconductor Introduction
R. Gentleman, F. Hahne, S. Falcon, M. Morgan

3. Processing Affymetrix Expression Data
R. Gentleman, W. Huber

4. Two Color Arrays
Florian Hahne, Wolfgang Huber

5. Fold Changes, Log Ratios, Background Correction, Shrinkage Estimation, and Variance Stabilization
W. Huber

6. Easy Differential Expression
F. Hahne, W. Huber

7. Differential Expression
W. Huber, D. Scholtens, F. Hahne, A. Heydebreck

8. Annotation and Metadata
W. Huber, F. Hahne

9. Supervised Machine Learning
R. Gentleman, W. Huber, V. J. Carey

10. Unsupervised Machine Learning
R. Gentleman, V. J. Carey

11. Using Graphs for Interactome Data
T. Chiang, S. Falcon, F. Hahne, W. Huber

12. Graph Layout
F. Hahne, W. Huber, R. Gentleman

13. Gene Set Enrichment Analysis
R. Gentleman, M. Morgan, W. Huber

14. Hypergeometric Testing Used for Gene Set Enrichment Analysis
S. Falcon, R. Gentleman

15. Solutions to Exercises
Florian Hahne, Wolfgang Huber, Robert Gentleman, Seth Falcon

Keywords: Statistics, Statistics for Life Sciences, Medicine, Health Sciences, Computational Biology/Bioinformatics, Bioinformatics, Mathematical Biology in General