Figure 4.

Log₁₀ of mean MAS 5.0 present/absent P value versus mean log₂ expression value. (a) Plot of log₁₀ mean MAS 5.0 present/absent P value versus mean log₂ expression value for control (C) replicates in the GoldenSpike dataset. The default P values for absent (0.06) and marginal (0.04) are marked with vertical lines (blue), and suggested expression value cutoffs (99% probesets with P values > 0.06 are below the log₂ cutoff) are marked by a dotted horizontal line (green). (b) ROC curves for C replicates using the best performing expression value method (black) and MAS 5.0 P values (red). Vertical lines correspond to the false positive rate of cutoff values suggested in (a). (c) Plot of log₁₀ of mean MAS 5.0 present/absent P value versus mean log₂ expression value for experimental replicates in the Latin-Square dataset. There are 42 spiked-in transcripts that can be aligned to probesets across a range of 14 different concentrations. The number of probesets called absent (MAS 5.0 P value < 0.06) is marked in the legend. Lines are as in (a).