( s test plan were deliberately chosen at...)The New Affymetrix GeneChip Scanner 3000

s test plan were deliberately chosen at levels close to the limit of detection. These concentrations were selected to challenge scanner performance with samples that represent low-level expression across a range of concentrations. Thus, certain spiked transcript comparisons appear to result in lower accuracy for both scanner types (Figure 5, 0.75 pM versus 1.50 pM and 0.00 pM versus 0.75 pM). The range of Increase call accuracy for 0.00 pM versus 0.75 pM was 81-91% for the GeneArray 2500, and 85-96% for the GeneChip Scanner 3000. For 0.75 pM versus 1.50 pM, the range was 59-75% for the GeneArray 2500 and 63-77% for the GeneChip Scanner 3000. This observation does not compromise the validity of the conclusion that both scanners perform similarly in most cases.

Accuracy of Target Spike Signal Log Ratio Comparisons

Signal Log Ratio (SLR) is a quantitative measure describing differential expression of a transcript across experimental conditions. It is derived from the one-step Tukeys Biweight method5 for Signal values for a given probe set compared across two experiments. SLR is the log2 of the ratio and is calculated by the MAS analysis software. Therefore, a SLR equal to 1 or -1 is equivalent to a two-fold increase or decrease in expression, respectively.

For comparison analyses between different target spike concentrations, there is an expected SLR for each of the 53 transcripts. For each scanner, the SLR analysis was performed for all concentration comparisons for which a SLR could be predicted.

Figure 6 illustrates the average SLR generated on HG-U133A probe arrays for target spike concentrations where pair-wise comparisons result in a SLR equal to 1 (0.75 pM versus 1.50 pM and 1.50 pM versus 3.00 pM). The SLR shown was calculated for all possible pair-wise comparisons of three replicates at two concentrations resulting in nine comparison analyses. Error bars represent one standard deviati
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