This brief description is primarily a guide to academic groups who plan on setting up a microarray data analysis pipeline. BASE (BioArray Software Environment, http://base.thep.lu.se) is an open-source platform for archiving, analysis and visualizing of microarray data. It is used at the ACGT Microarray facility where cDNA microarray slides are produced with a GenIII Spotter (Molecular Dynamics) and fluorescent images of slides are captured with a GenePix 4000B scanner (Axon Instruments) (http://fabinet.up.ac.za/microarray ). For this demonstration, gene expression levels of a susceptible mutant and resistant wild-type Arabidopsis plants were compared using 2-colour Cy-dye hybridization to microarrays spotted with ~500 Arabidopsis cDNA’s related to the defense response. Signal intensities were quantified with ArrayVision (Imaging Research Inc.) and raw data measurements imported into BASE. Experiments were defined and set up in BASE with extensive annotations for each step of the process. After filtering out artifacts, data was normalized. Using BASE, it was shown that 365 reporters had detectable data available for analysis. Of these, 86 reporters showed more than 2-fold difference in expression levels in the mutant Arabidopsis plants.