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Table 4 Performance metrics on differentially expressed (DE) plasmodes

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

edgeR robust DF = 50 edgeR robust DF = 10 edgeR robust DF = 4 edgeR robust \( \mathrm{D}\mathrm{F} = \widehat{DF} \) edgeR classic \( \mathrm{D}\mathrm{F} = \widehat{DF} \) DESEQ2
Power - All transcripts
0.6495 a 0.6275 b 0.6215 b 0.6229 b 0.5704 c 0.5418 d
(0.00610) (0.00610) (0.00463) (0.00463) (0.00435) (0.00435)
Power - Low-count transcripts
0.3922 a 0.3692 b 0.3657 b 0.3677 b 0.2647 c 0.1785 d
(0.00120) (0.00120) (0.00010) (0.00010) (0.00008) (0.00008)
Precision - All transcripts
0.3607 a 0.4393 b 0.5218 c 0.5323 c 0.6321 d 0.6586 e
(0.00792) (0.01153) (0.01192) (0.01114) (0.00589) (0.00371)
Precision - Low-count transcripts
0.1800 a 0.2289 b 0.2904 c 0.2963 c 0.3605 d 0.3915 e
(0.00811) (0.01305) (0.01432) (0.01378) (0.01363) (0.01727)
NPV - All transcripts
0.9917 a 0.9915 a 0.9915 a 0.9915 a 0.9902 b 0.9891 c
(0.00016) (0.00016) (0.00016) (0.00016) (0.00016) (0.00016)
NPV - Low-count transcripts
0.9917 a 0.9915 a 0.9914 a 0.9915 a 0.9902 b 0.9891 c
(0.00016) (0.00016) (0.00016) (0.00016) (0.00016) (0.00016)
Accuracy - All transcripts
0.9718 a 0.9778 b 0.9821 b 0.9826 c 0.9858 d 0.9862 e
(0.00080) (0.00080) (0.00024) (0.00024) (0.00012) (0.00014)
Accuracy - Low-count transcripts
0.9679 a 0.9744 b 0.9794 c 0.9798 c 0.9841 d 0.9855 e
(0.00122) (0.00122) (0.00079) (0.00079) (0.00028) (0.00028)
FPR - All transcripts
0.0221 a 0.0155 b 0.011 b 0.0106 c 0.0063 d 0.0053 e
(0.00086) (0.00086) (0.00024) (0.00024) (0.00001) (0.00010)
FPR - Low-count transcripts
0.0244 a 0.0175 b 0.0124 c 0.0121 c 0.0063 d 0.0037 e
(0.00128) (0.00128) (0.00082) (0.00082) (0.00019) (0.00019)
  1. Least square mean estimates (and corresponding SEM, shown in parentheses) for true positive rate (TPR; i.e. power), positive predictive value (PPV; i.e. precision), negative predictive value (NPV), accuracy and false positive rate (FPR) for differential expression at FDR = 0.05 on all transcripts and on low-count transcripts yielded by DESeq2, EdgeR classic or EdgeR robust, implemented on DE plasmodes of RNA-seq data. a,b,c,d,e, indicate significant differences (Tukey-Kramer adjusted P < 0.05) within a row