There are two general methods for making gene-expression microarrays: one is to hybridize a single test set of labeled targets to the probe, and measure the background-subtracted intensity at each probe site, the other is to hybridize both a test and a reference set of differentially labeled targets to a single detector array, and measure the ratio of the background-subtracted intensities at each probe site. Which method is better depends on the variability in the cell system and the random factors resulting from the microarray technology. It also depends on the purpose for which the microarray is being used. Classification is a fundamental application and it is the one considered here.