Demos & Downloads

Demos

• Graphical Reporting with Insightful ArrayAnalyzer

Downloads

• Data Libraries for Affymetrix Microarrays
• "Local pooled error test for identifying differentially expressed genes with a small number of replicated microarrays". [PDF]
• S+ArrayAnalyzer User's Guide [PDF] 12MB File. Caution: Lengthy download
• S+ArrayAnalyzer Datasheet [PDF]
• Statistical Issues in Microarray Experiments [PDF]
• Model-based Clustering Library for S-PLUS
• S+ArrayAnalyzer 2.0 User's Guide

Papers & Presentations

• BioInformatics Article: Local-pooled-error test for identifying differentially expressed genes with a small number of replicated micorarrays
  
  
• Score Tests for Association of Traits with Haplotypes when Linkage Phase is Ambiguous [PDF]
  
  
• Differential Expression, Class Discovery and Class Prediction using S-PLUS and S+ ArrayAnalyzer [PDF]
  
  
• Natural killer cells distinguish innocuous and destructive forms of pancreatic islet autoimmunity [Abstract]
  
  
• Pan, Wei, Lin, Jizhen, Le Chap T, Model-based cluster analysis of microarray gene-expression data. Genome Biology 2002, 3. [PDF]
  
  
• Kuonen, Diego, Challenges in Bioinformatics for Statistical Data Miners. Bulletin of the Swiss Statistical Society (2003) 46: 10-17. [PDF]
  
  
• Do, Hong-Hai, Kirsten, Toralf, Rahm, Erhard, Comparative evaluation of microarray-based gene expression databases. University of Leipzig, Germany [PDF]
  
  
• Working Group 1: Databases and Data Integration. Poster by Erhard Rahm, Hong-Hai Do, and Toralf Kirsten, Interdisciplinary Centre for Bioinformatics, University of Leipzig [PDF]
  
  
• S-PLUS Gene Poster [PDF]

• The Analysis of Gene Expression Data
  Giovanni Parmigiani, Elizabeth S. Garrett, Rafael A. Irizarry, Scott L. Zeger
• Data Analysis Tools for DNA Microarrays
  Sorin Draghici Wayne State University, Detroit, Michigan, USA
  Includes FREE trial Cd of S+ArrayAnalyzer Desktop!

Helpful Links:

S-PLUS Software:

• haplo.score, by Dan Shaid
• OOMAL, MDAnderson
• Pan et al. (2002) experimental design tools
• Newton et al. (2001) empirical Bayes model
• Fraley and Raftery, (2002) Model based clustering methods
• Do (2002) and Hastie and Tibshirani (2002) Gene Shaving and Cluster Analysis methods
• Ripley (2002) Support vector machines and other supervised and unsupervised learning methods
• Tibshirani, Hastie, Narashiman and Chu (2002) Prediction Analysis for Microarrays
  

Links to sites with other Sofware:

• Onto-Express http://vortex.cs.wayne.edu/Projects.html
  
• David: Ease http://david.niaid.nih.gov/david/ease.htm
  
• AmiGo Browser http://www.godatabase.org/cgi-bin/amigo/go.cgi
  

Genomics Resources:

• NCBI

Gene Research:

• Distinct Types of Diffuse Large B-Cell Lymphoma dentified by Gene Expression Profiling by Alizadeh et al.