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Table 2 Classification rules to compute performance metrics

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

  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
  1. 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