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Table 3 Estimated false positive rates (FPR) on null 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
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)
  1. 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