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

set effects in the scanner hardware. Immediately prior to each scan, the system shutters the photomultiplier tube in order to produce a dark scan. The dark signal is the cumulative result of all of the electronic noise and offsets in the system at that time. The returned signal is measured and characterized as to offset (average value) and noise (peak-to-peak envelope). A proprietary algorithm is used to calculate an appropriate system control voltage. When properly adjusted, the lower boundary of the system noise envelope can be driven very close to zero; in fact, only one or two data samples per thousand will be zero or lower. This performance is sufficient to satisfy the requirement for positive, non-zero data values while leaving the largest possible range available for fluorescence signal acquisition. An infrequent, zero-valued pixel does not cause any adverse effect on the data analysis. Figure 4 shows a dark line-scan capture. The GeneChip Scanner 3000 delivers this performance consistently, scan after scan, month after month.

AUTO-SET LASER POWER

One challenge of dealing with lasers is compensating for changes in laser intensity. Variables, such as ambient temperature, dust accumulation on optical component surfaces, and aging of the laser, are among some of the factors that cause system gain drift, thereby affecting scanner vs. time and scanner-to-scanner consistency. The GeneChip Scanner 3000 employs an Auto-Set Laser Power feature. Excitation laser power is accurately sampled immediately prior to every scan and, if necessary, precisely adjusted to the proper value for that assay.

Conclusion

The advanced design improvements described in this technical note that are incorporated in the Affymetrix GeneChip Scanner 3000 result in significant improvements in scan speed, signal resolution, noise, and dynamic range, as well as a significant reduction in lab b
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