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Table 1 Top ten genes originally calculated using S/N (for edgeR-normalized data; first ten rows) and top ten genes calculated using FDR for DE (edgeR P values; second ten rows). The table includes the counts-per-million table (A = GM12892 and B = H1-hESC), S/N and estimated false discovery rate (FDR) for edgeR and limma-voom for the ENCODE dataset comparing three replicates of GM12892 to four replicates of H1-hESC

From: Do count-based differential expression methods perform poorly when genes are expressed in only one condition?

Id A1 A2 A3 B1 B2 B3 B4 edgeR S/N edgeR FDR voom S/N voom FDR
MIPOL1 0.0 0.0 0.0 237.1 232.5 226.0 227.5 45.75 7.47e −31 3.79 3.32e −07
AQP4 0.0 0.0 0.0 46.1 45.0 46.7 44.4 43.87 1.44e −14 3.90 1.99e −06
FAM19A4 0.0 0.0 0.0 142.1 131.1 143.8 131.4 20.21 1.91e −24 4.06 4.72e −07
C17orf66 2.3 2.1 2.1 0.0 0.0 0.0 0.0 16.96 1.89e −02 2.72 7.40e −04
TM4SF19 3.5 3.2 3.2 0.0 0.0 0.0 0.0 16.96 3.00e −03 2.72 2.39e −04
SOX1 0.0 0.0 0.0 7.5 6.7 6.5 6.3 13.02 8.37e −05 4.33 1.27e −04
HPGD 0.0 0.0 0.0 22.6 21.0 19.6 19.0 12.97 5.08e −09 4.56 7.48e −06
LOC100131176 0.0 0.0 0.0 17.9 15.3 18.7 17.2 12.02 5.14e −08 3.51 1.49e −05
ZNF385D 0.0 0.0 0.0 135.5 155.0 155.0 132.3 11.80 2.60e −25 4.67 3.70e −07
NPY1R 0.0 0.0 0.0 209.8 179.9 179.3 208.5 11.38 1.33e −27 2.95 6.77e −07
PLEK 25 082.8 12 622.5 11 394.8 0.0 0.0 0.0 0.0 2.16 1.79e −216 16.11 9.36e −09
MS4A1 25 455.1 14 937.7 12 886.8 0.0 0.0 0.0 0.0 2.63 2.62e −215 7.26 1.60e −08
SLAMF1 7 407.2 4 859.3 4 283.2 0.0 0.0 0.0 0.0 3.32 2.98e −165 5.11 2.53e −08
CCL3 11 057.5 3 413.1 3 544.1 0.0 0.0 0.0 0.0 1.37 4.62e −165 5.13 2.15e −08
FCRLA 7 742.0 2 979.1 3 879.8 0.0 0.0 0.0 0.0 1.92 1.01e −161 6.08 1.84e −08
RGS1 9 939.5 9 967.3 7 741.6 0.0 0.0 0.0 0.0 7.22 4.53e −159 2.66 1.44e −07
DPPA4 0.0 0.0 0.0 14 580.2 15 215.1 14 745.3 10 617.3 6.47 2.37e −158 12.02 1.84e −08
TDGF1 0.0 0.0 0.0 15 699.8 15 481.1 13 374.5 8 522.5 3.98 6.37e −157 15.48 1.84e −08
SFRP2 0.0 0.0 0.0 14 673.3 15 229.5 13 067.2 7 234.4 3.43 1.84e −153 9.87 2.15e −08
BLK 9 943.0 2 954.7 2 351.8 0.0 0.0 0.0 0.0 1.20 2.98e −147 3.28 5.17e −08