PreP is a standalone full-interactive graphical suite for the pre-processing of gene expression data that aims at identify and remove sources of systematic and random variation in the measured data, other than differential expression. PrepP integrates a variety of analytical tools that in some cases can be applied in any context (such as the normalization -adjusting and ratio scaling). Other techniques require some specific conditions (e.g. gene replication). In any case, once the error has been removed as much as possible, the quantity of interest for each spot is the ratio of the amounts of label dye in the two channels, the target/control ratio.