Carl Troein, Johan Vallon-Christersson and Lao H. Saal An introduction to BASE To appear in Methods in Enzymology 441, DNA Microarrays Part B: Databases and Statistics (2006) Abstract: BASE is a web-based software package for storing, searching and analyzing locally generated microarray data and information surrounding the microarray production. The workflow begins in sample management and, optionally, microtiter plate tracking, and ends in visualization and analysis of entire experiments. The relative ease with which new analysis plug-ins can be added has given rise to a plethora of third-party tools, and the licensing terms (GNU GPL) encourage local modifications of the software. This introduction to BASE describes the basics of working with the software, both in general and in more detail for the various parts. It also provides some hints about more advanced usage, and a section on what is needed to set up your own BASE server. The information is current as of BASE version 1.2.17b, which was released on November 6, 2005. LU TP 06-02