Michael OConnell, Adam Diaz, David
Henderson, Jim Schimert
Insightful Corporation
S+ArrayAnalyzer is a microarray data analysis software solution developed in collaboration with BioConductor package developers and deployed with S-PLUS and S-PLUS Server. It includes methods for data access, probe-level summary, QA/diagnostics, filtering, normalization, differential expression testing, class discovery, class prediction, machine learning, annotation and gene list management. Analysis results are reported using S+Graphlets, lightweight web applets that include local drilldown and zoom, and connection to metadata on mouseover and click. S+ArrayAnalyzer is extendable using S-PLUS scripts, and (well-documented) C++, Java, SOAP, JavaServer Pages Tag API's. S+ArrayAnalyzer runs on Windows, Linux, and Solaris and includes web (server) and desktop deployment options.
This workshop covers worked examples on (a) differential expression (probe-level analysis, filtering (e.g. with GO terms), linear modeling, gene list management and annotation) using time course and 2-factor designs; and, as time permits (b) analysis of clinical and expression data for identification of biomarkers using resampled Cox regression and machine learning methods.
The workshop will be run using S+ArrayAnalyzer on Windows; attendees are encouraged to bring a Windows laptop with as much RAM as possible.