Figure 2.

MAS 5.0 present/absent calls. (a) The average frequency of P values of empty probesets generated by the MAS 5.0 present/absent algorithm when τ = 0.015 (solid black line) and when τ = 0 (dotted line). The average was taken over the six samples. The percentage of central nucleotides in PM probes for empty probesets with P values < 0.06, for all empty probesets (similar percentages are present in all probesets), and for empty probesets with P values > 0.94 are shown. (b) P values generated with the Wilcoxon signed rank test for random empty probesets. The PM-MM probe-pairs from empty probesets with fewer than six alignment errors to any transcript in the GoldenSpike dataset were randomly re-assembled into probesets based on the central nucleotide (for example, only central T nucleotides in the PM probes). Symbols and lines are colored according to the central nucleotide.