( r the GeneArray 2500. This T...)The New Affymetrix GeneChip Scanner 3000

This Technical Note details a set of controlled comparison experiments between the new GeneChip Scanner 3000 and the existing GeneArray 2500. The results demonstrate conclusively that the GeneChip Scanner 3000 meets or exceeds performance standards for the GeneArray 2500 in multiple independent comparisons.

Experimental Design

Overview

The newly designed GeneChip Scanner 3000 was developed to perform equivalently to or better than the existing GeneArray 2500. To evaluate the GeneChip Scanner 3000, two comprehensive test plans were executed to compare the GeneChip Scanner 3000 to the GeneArray 2500. These test plans were similar in that they shared common objectives regarding instrument performance:

Identify differences in global GeneChip probe array metrics, such as percent Present Calls, False Change between replicates, and correlation coefficients from Signal values. (Detailed in this Technical Note.)
Identify differences in the ability of the scanners to detect and quantify exogenous spiked transcripts in a complex cRNA target background, considering metrics such as Detection call accuracy, Change call accuracy, and Signal Log Ratio accuracy. (Detailed in this Technical Note.)
Survey customer satisfaction for the GeneChip Scanner 3000. (Detailed in the Affymetrix GeneChip Scanner 3000 Specification Sheet and other marketing materials.)

Both test plans involved acquiring data with both the GeneChip Scanner 3000 and GeneArray 2500 using the same GeneChip probe array scanned in both instruments. Any differences observed were due exclusively to the scanners. All analyses were conducted with the Affymetrix Microarray Suite 5.0 (MAS) software^{1, 2, 3.}

Beta Test Plan

test plan compared the performance of six pairs of scann
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