Differential Expression and Biomarker Identification using S+ArrayAnalyzer 2.1

S-PLUS 7 Enterprise Workbench and Server (Web) Deployment

Presented: September 8th, 2005

Speakers: Michael O'Connell and David Henderson of Insightful Corp., and Wei Ding of Schering Plough

View the archived Web cast.

Helpful Links:

• Web cast presentation [PDF]
• S+ArrayAnalyzer datasheet [PDF]
• Clinical development Web site
• Insightful Research Libraries
• Case studies in S-PLUS: Millard and Krause
• S-PLUS books
• S+Graphlets Info
• Wei Ding 2004 UC presentation: Exploring Expression Data Using S+ArrayAnalyzer
• Training
• S-PLUS newsgroup (email to "s-news-request@lists.biostat.wustl.edu". with "subscribe s-news" in the body of the email
• StatLib (http://lib.stat.cmu.edu/S/)

Abstract: This seminar describes workflows for statistical analysis of microarray and clinical data for the identification of differentially expressed genes and biomarkers.

Particular attention will be given to the analysis of two-sample and multi-level phenotype expression data and the workflows described include careful attention to all facets of microarray/clinical data analysis including pre-processing (normalization, probe-level summary), differential expression testing (multi-factor linear models), class discovery (clustering), class prediction (machine learning), gene-list management and annotation (pathway connections). Machine learning biomarker analysis with feature selection and filtering using tree ensembles and (recursive) support vector machines will be described.

Exploratory and regulated (e.g. 21 CFR 11) environments will be addressed in context. The workflows and analyses will be presented from the perspective of the end-user scientist working in a web user interface and/or DecisionSite desktop interface, and from the perspective of the analyst and computational biologist working in the S-PLUS 7 workbench and/or server environment. Integration and web deployment will be described by way of case study in a real world setting at Schering Plough. This case study features S+ArrayAnalyzer deployed through S-PLUS Server in the Linux environment using jsp and S-PLUS Server tag libraries.

Michael O'Connell, Ph.D., Insightful Corporation

Michael O'Connell, Ph.D., is director of Life Science Solutions at Insightful Corp. He has more than 15 years experience in the medical device, informatics and health-care statistics arena, having published more than 30 papers on statistics, data mining and health-care applications. This has included statistical methods work in the areas of non-parametric regression, experimental design, calibration and mixed models; and applications such as DNA amplification, diagnostics, microarray data analysis and safety data mining.

Wei Ding, Schering Plough

Wei Ding received his B.S from the University of Science and Technology of China, and Ph.D. in Biophyiscs from the State University of New York at Stony Brook. After working as Fogarty Fellow in the National Center for Biotechnology Information (NCBI), he joined the Bioinformatics group at the Schering-Plough Research Institute. He is also an adjunct professor in the Department of Biological Sciences at Kean University. His research interests include genomics data mining and functional analysis, application of statistics to the study of gene expression, and systems biology. He is also responsible for the development of statistical tools for functional analysis of microarray, proteomics, and genomics data.