Inferential considerations for low-count RNA-seq transcripts: a case study on the dominant prairie grass Andropogon gerardii

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

ISSN: 1471-2164