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

e across the image field because of misalignment. On any given scanner, the fluorescent intensity gradient can vary from edge to edge. The gradient may have opposite signs and/or unequal slopes. The implication of this characteristic is that a probeby- probe gain matching of two (or more) scanners is almost impossible. Gain calibration procedures can only match the average intensity of reference fluorescence material to an average target value. Even if the gain matching procedure was perfect, comparison of specific features from images of the same array scanned on different scanners can exhibit absolute intensity mismatches of 30% or more.

It should be noted that biological performance is not adversely affected, due to the Perfect Match/Mis-Match strategy (referred to as PM/MM) of the array design, coupled with robust Affymetrix Microarray Suite expression algorithms.

Affymetrix GeneChip Scanner 3000 System

FLYING OBJECTIVE LENS

The Affymetrix patented flying objective technology represents a radical departure from the previous GeneChip array scanner that employed pre-objective line-scan technology (Figure 2). Affymetrix patented Flying Objective Lens (FOL) technology addresses all of the above issues with a simple, yet elegant, opto-mechanical design. Scan speed is increased, optical distortion is decreased, and emission path alignment robustness is ensured by simultaneously moving the scanning mirrors and the objective lens. The scan motion, corresponding to the fast, or X-axis, is achieved by rotating a scan-arm (objective lens and mirror assembly) around a section of the optical path located between two mirrors, one fixed to the internal optics bench, the other in the center of the scan-arm. This optical structure creates a periscope, whose optical path is co-axial with the axis of rotation of the galvanometer, and carries both excitation (forward path) and emission
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