Bioconductor Case Studies

• Main Authors: Hahne, Florian (Author), Huber, Wolfgang (Author), Gentleman, Robert (Author), Falcon, Seth (Author)
• Corporate Author: SpringerLink (Online service)
• Format: Electronic eBook
• Language: English
• Published: New York, NY : Springer New York, 2008.
• Edition: 1.
• Series: Use R!
• Subjects: Life sciences.; Bioinformatics.; Biomathematics.; Statistics.; Life Sciences.; Life Sciences, general.; Statistics for Life Sciences, Medicine, Health Sciences.; Computational Biology/Bioinformatics.; Mathematical and Computational Biology.

Bioconductor 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 Biocon...

Table of Contents:

• The ALL Dataset
• R and Bioconductor Introduction
• Processing Affymetrix Expression Data
• Two Color Arrays
• Fold Changes, Log Ratios, Background Correction, Shrinkage Estimation, and Variance Stabilization
• Easy Differential Expression
• Differential Expression
• Annotation and Metadata
• Supervised Machine Learning
• Unsupervised Machine Learning
• Using Graphs for Interactome Data
• Graph Layout
• Gene Set Enrichment Analysis
• Hypergeometric Testing Used for Gene Set Enrichment Analysis
• Solutions to Exercises.