Table 3.

Estimated false positive rates (FPR) on null 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
FPR - All transcripts
0.0177 a	0.0093 b	0.0063 c	0.0061 c	0.0042 d	0.0031 e
(0.00040)	(0.00040)	(0.00040)	(0.00040)	(0.00040)	(0.00040)
FPR - Low-count transcripts
0.0176 a	0.0094 b	0.0064 c	0.0063 c	0.0043 d	0.0032 e
(0.00037)	(0.00037)	(0.00037)	(0.00037)	(0.00037)	(0.00037)

Least square mean estimates (and corresponding SEM, shown in parentheses) of FPR for differential expression at FDR = 0.05 on all transcripts and on low-count transcripts based on DESeq2, EdgeR classic and EdgeR robust, implemented on null plasmodes of RNA-seq data. a,b,c,d,e, indicate significant differences (Tukey-Kramer adjusted P < 0.05) within a row