An S-PLUS Library for the Analysis and Visualization of Differential Expression

This chapter describes a genomics library for S-PLUS® 6. One focus of the work involves the testing of hypotheses regarding differential expression. In this area, we provide methods and S-PLUS functions for expression error estimation based on pooling errors within genes and between duplicate arrays for genes in which expression values are similar. This is motivated by the observation that errors between duplicates vary as a function of the average gene expression intensity and by the fact that many gene expression studies are implemented with a limited number of replicated arrays (Lee, 2002).Our clustering and visualization methods take advantage of S-PLUS GraphletsTM, lightweight applets that are simply created using the Java and XML-based graphics classes and the java. graph graphics device that are new to S-PLUS 6. In addition to providing interactive graphs in a Web browser, the Graphlets enable connection to gene-information databases such as NCBI GenBank. Such connectivity facilitates incorporation of additional annotation information into the graphical and tabular summaries via database querying on the URL. The S-PLUS 6 genomics library is available at www. insightful.com/arrayAnalyzer. This site also provides updates regarding ongoing work in genomics and related areas at Insightful.