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.
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 bPage: All 1 2 3 4 5 6 7 8 9 10 Related biology technology :1
. Fine Tuning Your Data Analysis:
Tunable Parameters of the Affymetrix Expression Analysis Statistical Algorithms2
. The New Affymetrix GeneChip Scanner 30003
. GeneChip Sample Cleanup Module for cleanup of cDNA and in vitro
. New statistical algorithms for Monitoring Gene Expression on GeneChip® Probe Arrays5
. General Notes on Primer Design in PCR*6
. siRNA Design Guidelines7
. Avoid siRNA Design Altogether!8
. Cenix-Designed siRNAs for 95% of Human and Mouse Genomes9
. Designing a Successful qRT-PCR Experiment10
. Designing a Better siRNA11
. Designing Controls for siRNA
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