Data are normalized to mean ratio intensity.

The arrays are scanned immediately. Each comparison is performed in duplicate. Fluorescent cDNA bound to the microarray is detected with a GenePix 4000 microarray scanner (Axon Instruments, Foster City, CA), using the GenePix 4000 software package to quantify microarray fluorescence.

Intensity values are adjusted by subtracting surrounding background from spots. The median of spot intensities is corrected for background. To eliminate signals that are most prone to estimation error, any spot is excluded from analysis if both the Cy3 and Cy5 mean fluorescence signals are within two standard deviations of the mean background signals for that spot. This procedure avoids artificially inflated measurements of expression due to low signals. Additional to eliminating flagged spots, spots are also visually inspected and flawed ones discarded from the analysis.