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

o optical signal (i.e., dark) input. Prior systems added a small, positive input signal to the fluorescence data in order to ensure that the digitizing system would not see negative or zero data values. When presented to the digitizer, negative values are clipped to zero, resulting in loss of the ability to see small signals. If a sufficient number of zeros cluster together, average value and noise calculations of probes will be corrupted. This positive signal, referred to as offset, is subject to drift with time and temperature. The offset value must, therefore, be set high enough to guarantee that the system returns positive, non-zero values over all time and environmental conditions. Since the offset signal is not signal related it provides no useful data value; however, it uses up some of the available range of data values. Prior scanner systems exhibited system offsets of 30 to 50 counts but, in some cases, could range up to 100 counts.

OFFSET EXAMPLE

Consider the implementation of a vertical measurement system where you only have access to a meter stick 1,000mm in length (dynamic range), divided into 1mm increments (resolution). A further requirement is that the system must be freestanding because both of your hands are required to hold the object to be measured. The simplest solution would be to poke the meter stick sufficiently into the ground to allow it to stand uprightsay 50mm. The meter stick remains 1,000mm in length, but in this configuration only 950mm extends above ground available for use as a measurement tool. The resolution of your measurement system is unchanged at 1mm but the dynamic range of the system has been reduced to 950mm.

THE GENECHIP SCANNER 3000

The GeneChip Scanner 3000 Auto-Zero sub-system provides typical instrumentation system offset performance of around 20 counts. The new Auto-Zero sub-system is designed to measure, and compensate for, long-term off
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