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Fine Tuning Your Data Analysis:,,, Tunable Parameters of the Affymetrix Expression Analysis Statistical Algorithms

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I.C. Detection p-value: tau Discrimination threshold

As mentioned in Section I.A. (and in further detail in references 1 and 2), tau serves as the discrimination threshold against which individual probe pairs are tested for specific detection. This parameter is determined experimentally by measuring a large number of probe pair Discrimination Scores for transcripts that are known to be absent from a test sample. Unlike the alpha parameters, tau directly affects the calculation of Detection p-values. If tau is set lower than the default value (0.015 for 16-20 probe pair designs), the stringency of detection is relaxed, resulting in a shift in the distribution of p-values towards 0. If it is set higher than the default, the analysis becomes more stringent; a higher level of discrimination is required for specific detection, and the p-values are shifted towards 1.0.

Figure 4 shows how tau affects the percentages of Detection calls across an entire array. Moving tau above the default increases the stringency of detection, resulting in fewer genes detected as Present and Marginal, and additional genes as Absent. Conversely, moving tau below the default decreases the stringency of detection, allowing more genes to be called Present or Marginal, and fewer genes as Absent.

The effect on Detection p-values for individual probe sets can vary. Figure 5 shows Detection p-values for two transcripts expressed in a normal rat heart sample, as well as two exogenous spikes. A given transcripts Detection p-value responds in an individual way to changes in tau, since the p-value calculation is based on how individual

probe pairs in a probe set rank against tau. The curve for bioB exemplifies a low-level transcript; as tau is increased, its p-value crosses the alpha cutoffs, resulting in an Absent call. A rat transcript (gene1) also becomes undetected at the highest setting of tau (0.15)
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