Once a DNA array experiment has been designed and executed the data must be extracted and analyzed. That is, the signal from each address on the array must be measured and some method for determining and subtracting the background signal must be employed. However, because there are many different DNA array formats and platforms, and because hybridization signals can be generated with fluorescent- or radioactive-labeled targets, no single DNA array readout device is suitable for all purposes. Furthermore, many instruments with different advantages and disadvantages for different types of array formats are available. Therefore, since accurate data acquisition is a critical step of any array experiment, careful attention must be paid to the selection of data acquisition equipment.

Reading data from a fluorescent signal

All arrays that emit a fluorescent signal must be read with an instrument that provides a fluorescence excitation energy source and an efficient detector for the light emitted from the fluorophore incorporated into the target. Currently, the fluorophores most commonly used for incorporation into cDNA targets are Cy3 and Cy5. These are cyanine dyes commercially available as dUTP or dCTP conjugates. Cy3 is an orange dye with a light absorption maximum at 550 nm and an emission maximum at 581 nm. Cy5 is a far-red dye with a light absorption maximum at 649 nm and an emission maximum at 670 nm.