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

a acquisition electronics have been implemented using the latest generation of high-speed sampling analog-to-digital converters. The use of high-quality electronic components is critical; however, it is only part of the story. The best components in the world cannot differentiate between real signal from fluorescent emissions, and noise signal caused by radiated or conducted pick-up resulting from poor circuit implementation. Electrical pollution of signals can be caused by proximity to nearby conductors carrying dirty signals, local radio or television stations, or certain types of equipment plugged into the same power source. Sampled data are used to create a snapshot in time of the signal that is presented to the system regardless of its origin. Considerable design effort was put into the optimization of the data acquisition electronics packaging and printed circuit layout to ensure exceptional immunity from external noise sources. Affymetrix specifically custom- designed and continues to build this key sub-system in the manufacturing facility to ensure complete control of the design and manufacturing quality.

REDUCED MEASUREMENT NOISE

One of the biggest hurdles to getting accurate, high-quality, biological data is measurement noise. There are two main sources of system noiseInstrument and Process. Instrument-related sources include data acquisition electronics (previously discussed), laser output noise, optical nonuniformity, auto-fluorescence of optical components, etc. Process-related sources (that, in general, are not mitigated by scanner design elements) include sample contamination, non-specific binding of fluorophores to array features, and non-uniform hybridization. System noise, or total noise from all sources, causes signal measurement uncertainty, i.e., any given data sample may be inaccurate within the system noise band. Noise becomes a significant issue when measuring very small signals. Generally, when comparing instrum
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