9) TM4 Microarray Software Suite

Powerful specialized software is essential for managing, quantifying, and ultimately deriving scientific insight from results of a microarray experiment. We have developed a suite of software applications, known as TM4, to support such gene expression studies. The suite consists of open‐source tools for data managementandreporting,imageanalysis,normalizationandpipelinecontrol, and data mining and visualization. An integrated MIAME‐compliant MySQL database is included. This chapter describes each component of the suite and includes a sample analysis walk‐through.