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Some useful links:

Whitehead Genome Technology Core links to software useful for Data Analysis

Whitehead Genome Technology Core instructions on submitting data to GEO

OZONE MAP - Exposure to moderate or high levels of ozone is known to degrade the dye Cy5 to a level noticeable in two-color microarray experiments. Consider alternative scanning times for the Agilent scanner if there are high levels of ozone predicted (typical on hot summer days) or using Cy5 stabilizing reagents. courtesy WI-GTC