Figure 13

Performance measures for the combined method. (a) Plot of AUC scores for true positive rate (TPR) versus false positive rate (FPR) based on Cyber-T P-values for individual methods and q-values for the combined statistical methods (GOLD and ALCHEMY). True positives were FC > 1 probesets and mixed probesets that could be aligned to spiked-in transcripts. All other probesets are true negatives. Performance measures are based on a subset of probesets with present transcripts. Additional AUC scores were calculated using all probesets to show the influence of probesets with absent transcripts. (b) Plot of true q-values based on the calculated q-values of 0.10. (c)Methods used in the alchemy method; the order of processing is NSB correction/probe-level normalization/probe summary/probeset-level normalization.