Table 2.

Classification rules to compute performance metrics

	Transcripts not DE	Transcripts “spiked” for DE	Total
Transcripts not declared significantly DE	TN	FN	R0
Transcripts declared significantly DE	FP	TP	R1
Total	S0	S1	G

FP number of false positives (transcripts in S₀ set declared differentially expressed); TP number of true positives (transcripts in S₁ set declared differentially expressed); TN number of true negatives; FN number of false negatives; FPR, false positive rate = FP/S₀; TPR true positive rate or power = TP/S₁; PPV positive predictive value or precision = TP/R₁; NPV negative predictive value = TN/R₀; accuracy = (TP + TN)/G