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The Affymetrix GeneChip Scanner 3000,,, New Advances in Scanner Design for Superior Performance, Reliability, and Dynamic Range

nts in the system. Laser selection criteria include physical size, cost, reliability, lifespan, output power stability, noise, spot fidelity, pointing accuracy, etc. Gas lasers offer excellent beam characteristics and unit cost, but have size, power supply, and cooling requirements that create cost and complexity for system packaging design. On the other hand, solid-state lasers are highly reliable and provide stable, lownoise, high-quality beam characteristics, but at a higher cost. Because of the aggressive data quality and system reliability goals that were set for the GeneChip Scanner 3000, Affymetrix engineers ultimately chose a high-quality, solid state 532nm Diode-Pumped, Frequency Doubled Nd:YAG (Neodymium-doped Yttrium Aluminum Garnet) Green Laser (Figure 3).

Additionally, because it uses a solid-state laser, there is no need for an external laser power supply under the bench or for a special cooling system. The scanner optics are designed to condition the laser beam to deliver an excitation spot size of 3.5μm (measured at the 1/e points), resulting in a two-fold improvement in optical resolution, as compared to the previous generation of array scanners.

INCREASED DYNAMIC RANGE AND SIGNAL RESOLUTION

High-performance instrumentation must be able to accurately measure both very small and very large signals. This performance metric is referred to as dynamic range, and is usually specified as a ratio of the largest value of data that can be expressed divided by the smallest increment into which the data can be resolved or digitized.

The GeneChip Scanner 3000 is able to distinguish very low levels of fluorescence, due to its powerful new high-speed, 16-bit data acquisition system. A full 16 bits of resolution means that 65,535 different levels of fluorescence can now be resolveda 31% improvement in data precision over the 50,000 level capability delivered by the previous scanner. The dat
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