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

Table 4 Performance metrics on differentially expressed (DE) plasmodes

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)

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

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