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Figure 5 | Genome Biology

Figure 5

From: Correcting for sequence biases in present/absent calls

Figure 5

AUC performance of alternative methods. (a) AUC scores for the MAS 5.0 present/absent algorithm when raw (black) or GC-RMA transformed (red) PM and MM are used. Scores were generated with a range of Ï„ values. (b) AUC scores when MM probe values are replaced by a GC-RMA transformed PM value. The threshold values are based on the mean value of PM probes from probesets that have absent target transcripts. Scores using different stringencies of finding absent transcripts are shown (P > 0.06, black; P > 0.25, red; P > 0.50, green; P > 0.75, blue). (c) ROC curves based on MAS 5.0 present/absent P values when using raw probe values (gray), GC-RMA transformed probe values (black) and threshold probe values (blue dotted line) are shown. Green lines indicate the true (horizontal) and false (vertical) positive rate for the default P value cutoff (0.06) to separate 'marginally present' and absent transcripts using raw PM and MM values. AUC and ROC curves are based on the mean P value of control replicates.

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