Fig. 9. Comparison of call sensitivity profiles. Probe sets are comprised of N = 16 probe pairs selected by the heuristic method (yellow dots) and N = 11 (blue triangles) and N = 16 (red squares) probe pairs selected by the model-based method. N is the number of probe pairs in the probe set. Sensitivity and specificity values were determined for probe sets of 99 yeast genes in four replicate Latin square (probe selection test set) experiments (Rep). Sensitivity values are given for each base target [T] concentration. Algorithm parameters were adjusted to achieve the same specificity values for the three types of probe sets in a given comparison study. (A) Comparison of 2-fold change call sensitivity. Sensitivity is equal to the fraction of increase calls out of the total comparisons, where the target concentration is a 2-fold increase relative to the base concentration (twofoldRepPair). The number of total comparisons is 1,584 change calls (1 change call/twofoldRepPair ´ 16 twofoldRepPairs / gene ´ 99 genes). Specificity is equal to the average fraction of no change calls out the comparisons, where the target and base concentrations were the same. Algorithm parameters were adjusted to achieve specificities of 99.0%. (B) Detection call sensitivity profiles. Sensitivity is equal to the fraction of detection (present) calls out of a total of 396 calls (1 detection call / Rep ´4 Reps / gene ´99 genes), for the given concentration. Specificity is equal to the fraction not detected (absent) when [T] equals zero. Algorithm parameters were adjusted to achieve specificities of 93.2%.