Fig. 3

Classification analysis comparisons. a fraction of sequences identified as significantly active (BH-corrected P<0.05) by method and class of sequence. MPRAnalyze results both in control-based (red) and no-controls (orange) modes; empirical p values based on the mean ratio (blue) or aggregated ratio (green); DESeq2 results in collapsed mode (barcodes are summed within each batch, purple) or full mode (full data, light blue). Absolute number of active sequences is displayed on the bars. b Precision-Recall curve. Precision is based on performance on the negative controls, Recall is based on the total population of sequences, assuming all candidates are active. Error bars are ± the standard deviation of these measures across datasets. c Fraction of active sequences detected after re-running the analyses on 685 sequences from the Inoue-Kreimer dataset that were identified as active by MPRAnalyze (regular mode) and both DESeq2 modes, and the 200 controls from the same dataset. MPRAnalyze recapitulates the same results, finding that 100% of the candidates are active, whereas DESeq2 full only identifies 161 (23.5%) and DESeq2 collapsed completely fails to identify any active sequences