METHODS
AND SOFTWARE
edited by Giovanni Parmigiani, Elizabeth S Garrett, Rafael A Irizarry, Scott L Zeger,
from the Sidney
Kimmel Comprehensive Cancer Center at Johns Hopkins University
and the Department
of Biostatistics, Bloomberg School of Public Health, at Johns Hopkins
University
Published in March 2003 by Springer, NY
This book presents practical approaches for the analysis of data from gene expression microarrays. Each chapter describes the conceptual and methodological underpinning for a statistical tool and its implementation in software. Methods cover all aspects of statistical analysis of microarrays, from annotation and filtering to clustering and classification. Chapters are written by the developers of the software packages presented.
All software presented in the book free to academic users. The book includes coverage of various packages that are part of the Bioconductor project and several related R tools.
The materials presented
cover a range of software tools designed for varied audiences. Some chapters
describe simple menu-driven software in a user-friendly fashion, and are
designed to be accessible to microarray data analysts without formal quantitative
training. Most chapters are directed at microarray data analysts with master-level
training in computer science, biostatistics or bioinformatics. A minority
of more advanced chapters are intended for doctoral students and researchers.
| Chapter Title | Authors | Software | Related Reference(s) |
| Introduction | Garrett, Irizarry, Parmigiani, and Zeger | ||
| Gene Filtering and Annotation | Gentleman and Carey | http://www.bioconductor.org | |
| R packages for the analysis of cDNA microarray data | Dudoit and Yang | http://www.bioconductor.org | Dudoit
et al. (2002) JASA
Dudoit et al. (2001) Statistica Sinica Yang et al. (2001) Proceedings of SPIE Dudoit et al. (2002) In preparation |
| An R Package for Oligonucleotide Array Statistical Analysis | Irizarry, Gautier and Cope | affy | Irizarry et al. (2002) Submitted |
| DNA-Chip Analyzer (d-Chip) | Li and Wong | DCHIP | Li
and Wong (2001) PNAS
Li and Wong (2001) Genomebiology |
| Expression Profiler | Vilo, Kapushesky, Kemmeren, Sarkans and Brazma | Expression Profiler | http://industry.ebi.ac.uk/~vilo/Publications/ |
| An S-plus library for the Analysis of Microarray Data | Lee and O'Connell | S-PLUS 6 GENOMICS LIBRARY | |
| DRAGON and DRAGON View: Methods for the Annotation, Analysis and Visualization of Large-Scale Gene Expression Data | Bouton, Henry, Colantuoni and Pevsner | DRAGON | Bouton and Pevsner (2000) Bioinformatics |
| SNOMAD: User-Friendly Web Tools for the Standardization and NOrmalization of MicroArray Data | Colantuoni, Henry, Zeger and Pevsner | SNOMAD | Colantuoni et al. (2002) Submitted |
| Microarray analysis using the MicroArray Explorer | Lemkin, Thornwall and Evans | MAExplorer | |
| Parametric Empirical Bayes Methods for Micorarrays | Newton and Kendziorski | EBarrays | Kendziorski, C.M., M.A. Newton, H. Lan, and M.N. Gould (2003) |
| SAM thresholding and false discovery rates for detecting differential gene expression in DNA Microarrays | Storey and Tibshirani | SAM | Storey
(2002) JRSS-B
Tusher, Tibshirani and Chu (2001) PNAS |
| Adaptive Gene Picking with Microarray Data: Detecting Important Low Abundance Signals | Lin, Nadler, Lan, Attie and Yandell | Pickgene | Tech report |
| MAANOVA: a software package for the analysis of spotted cDNA microarray experiments | Wu, Kerr, Cui and Churchill | MAANOVA | |
| GeneClust | Do, Broom and Wen | GeneClust | |
| POE: Statistical Methods for Qualitative Analysis Of Expression | Garrett and Parmigiani | POE | A statistical framework for molecular classification in cancer |
| Bayesian Decomposition | Ochs | Bayesian Decomposition | Ochs et al. (1999) J. of Magnetic Resonance
Ochs et al. (2001) AIP Conf. Proceedings Ochs et al. (2001) Magnetic Resonance in Medicine Moloshok et. al. (2001) Bioinformatics |
| Cluster Analysis of Gene Expression Dynamics | Sebastiani, Ramoni and Kohane | CAGED | M.
Ramoni, P. Sebastiani and I.S. Kohane.
Cluster Analysis of Gene Expression Dynamics. Proc Nat Acad Sci USA. 99(14):9121-6. 2002. |
| Relevance Networks | Butte and Kohane | RelNet | Butte
and Kohane
Unsupervised Knowledge Discovery in Medical Databases Using Relevance Networks |
Microarray Expression Data Analysis References
Microarrays databases on the WWW
Microarrays Software Comparison
SMAWEHI: An R Library for Statistical Microarray Analysis