Maximization of signal derived from cDNA microarrays

Microarray technology is a powerful tool for generating expression data on a large number of genes simultaneously. However, as for any assay! it must be reproducible to give confidence in the results. Using a classical statis tical method-the factorial design of experiments-we have assessed the effec ts of different experimental factors in our system. Significant effects on signal were seen when the standard components were substituted with a diffe rent enzyme, fluorescent label. or RNA purification method. This has fed to the implementation of an improved procedure that maximizes signal without affecting the variability of the system. thus increasing the signal-to-nois e ratio. In addition, we were able to quantify the variability between micr oarrays and replicates within microarrays.