Amaratunga D., Cabrera J., Shkedy Z. Exploration and Analysis of DNA Microarray and Other High-Dimensional Data

2nd Edition. — John Wiley & Sons, Inc., Canada, 2014. — 346 p. — ISBN: 978-1-118-35633-3.In August 1999, at the Joint Statistical Meetings in Baltimore, two of us [DA & JC] were invited to present a paper on “The Analysis of DNA Microchip Data.” This was the first presentation in any Joint Statistical Meetings on the topic of DNA microarrays, as they are now called. In just a few years, the field has exploded and, in each of the recent Joint Statistical Meetings, there have been over a hundred presentations related to DNA microarrays!
The Baltimore paper outlined many of the issues that are still being discussed today, including intensity-dependent normalization, the use of methods that are robust to outliers, improving the sensitivity of the analysis by borrowing strength across genes, and interpretation of results in a way that is germane to the overall objectives of a study. However, there have been many developments since then, and this book represents our effort at organizing this material into a semicoherent whole.A Brief Introduction
Genomics Basics
Microarrays
Processing the Scanned Image
Preprocessing Microarray Data
Summarization
Two-Group Comparative Experiments
Model-Based Inference and Experimental Design Considerations
Analysis of Gene Sets
Pattern Discovery
Class Prediction
Protein Arrays