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Table 3 Performance evaluation under Study II (Setting 1), (G=5000, 500 DE gene) #

From: Confident difference criterion: a new Bayesian differentially expressed gene selection algorithm with applications

Method CDE CCDE CCEE FNR FPR FDR FNDR
twocri. (γ 0=0.4) 785.1(8.3) 465.6(2.5) 4180.5(7.6) 0.069(0.005) 0.071(0.002) 0.407(0.006) 0.008 (0.001)
(γ 0=0.6) 509.4(6.8) 421.3(4.6) 4411.9(4.1) 0.157(0.009) 0.019(0.001) 0.173(0.007) 0.018(0.001)
(ζ=0.05) 344.2(8.2) 328.8(6.3) 4484.6(2.6) 0.342(0.013) 0.003(0.001) 0.044(0.007) 0.037(0.001)
edgeR 1(ζ=0.05) 289.7(17.6) 278.1(16.5) 4488.3(3.6) 0.444(0.033) 0.003(0.001) 0.040(0.011) 0.047(0.003)
edgeR 2(ζ=0.05) 290.6(18.1) 276.4(16.8) 4485.8(3.8) 0.447(0.034) 0.003(0.001) 0.049(0.012) 0.047(0.003)
DESeq(ζ=0.05) 297.2(21.3) 265.9(18.4) 4468.7(5.6) 0.468(0.037) 0.007(0.001) 0.105(0.016) 0.050(0.002)
BaySeq(ζ=0.05) 203.1(22.8) 203.0(22.8) 4499.9(0.2) 0.594(0.046) 0.000(0.000) 0.000(0.001) 0.062(0.004)
NBPSeq(ζ=0.05) 248.3(20.5) 239.8(19.3) 4491.5(4.0) 0.520(0.039) 0.002(0.001) 0.034(0.015) 0.055(0.004)
EBSeq(ζ=0.05) 303.7(18.8) 257.7(14.9) 4454.0(6.8) 0.485(0.030) 0.010(0.002) 0.151(0.017) 0.052(0.003)
NOISeq(ζ=0.05) 303.1(19.1) 294.4(17.6) 4491.3(3.2) 0.411(0.035) 0.002(0.001) 0.028(0.010) 0.044(0.004)
SAMSeq(ζ=0.05) 134.2(45.2) 126.1(43.2) 4491.9(3.4) 0.748(0.086) 0.002(0.001) 0.061(0.022) 0.077(0.008)
TSPM(ζ=0.05) 85.4 (19.2) 58.7 (15.4) 4473.3(6.5) 0.883(0.031) 0.006(0.001) 0.316(0.056) 0.090(0.003)
  1. #Empirical estimates of the standard deviation were reported in the parentheses
  2. edgeR 1estimates the common dispersion parameter for all tags; edgeR 2 estimates the tag-wise dispersion parameters
  3. ζdenotes the FDR