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

ents, there is little, if any, difference in data quality when analyzing high-level (highly expressed) signals. Most of the differentiation in data quality is seen when comparing results obtained from analyzing lowlevel signals. The specification used to quantify this property is called Signal-to- Noise Ratio, sometimes abbreviated as S/N Ratio or SNR. Since noise in a practical instrument can approach, but never achieve, zero, there is a finite limit to the lowest level of signal that can, to a reasonable degree of certainty, be measured.

SNR EXAMPLE

The following example is a good way to understand these principles. How accurately can you measure the depth (i.e., Signal) of the ocean at two different locations? The first location is near the shore where the depth is about two feet; the second location is further out where the depth is about one hundred feet. Let us further assume that the water is choppy (Noise) with disturbances of two feet, peak to trough. Exactly how deep is the water when you are standing in two feet of water with two-foot, peak-to-trough waves rolling by? At any instant in time, two-foot waves add about a 50% uncertainty to your measurement accuracy.

Now sail out to water that is 100 feet deep. The same two-foot waves only introduce a 1% uncertainty, relative to the much deeper water. Likewise, the instrument noise-floor is significantly more dominant when measuring small signals versus large signals. The instrumentation noise floor in the GeneChip Scanner 3000 is below the expected biological noise-floor of the array itself.

Reduced Measurement Offset

PREVIOUS SYSTEMS

While noise limits the ability of an electrooptical measurement system to accurately quantify low-level signals, offset reduces the available dynamic range of the system. Offset is the average value returned by the acquisition system with n
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