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Table 4 Performance evaluation under Study II (Setting II), (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) 654.6(5.4) 460.9(2.3) 4306.3(5.2) 0.078(0.005) 0.043(0.001) 0.295(0.006) 0.009(0.000)
(γ 0=0.6) 490.0(3.9) 434.1(2.4) 4444.2(3.4) 0.132(0.005) 0.012(0.001) 0.114(0.006) 0.014(0.001)
(ζ=0.05) 415.7(5.0) 400.6(3.5) 4484.9(2.7) 0.199(0.007) 0.003(0.001) 0.036(0.006) 0.022(0.001)
edgeR 1(ζ=0.05) 420.0(8.6) 411.7(8.4) 4491.7(2.8) 0.177(0.017) 0.002(0.001) 0.020(0.001) 0.020(0.002)
edgeR 2(ζ=0.05) 399.4(10.2) 386.3(9.8) 4486.9(4.6) 0.227(0.020) 0.003(0.001) 0.033(0.011) 0.025(0.002)
DESeq(ζ=0.05) 443.6(15.9) 409.3(15.1) 4465.8(5.3) 0.181(0.030) 0.008(0.001) 0.077(0.011) 0.020(0.003)
BaySeq(ζ=0.05) 331.0(15.5) 327.0(14.9) 4496.0(2.2) 0.346(0.030) 0.001(0.000) 0.012(0.006) 0.037(0.003)
NBPSeq(ζ=0.05) 422.3(7.9) 412.7(7.9) 4490.4(3.1) 0.175(0.016) 0.002(0.001) 0.023(0.007) 0.019(0.002)
EBSeq(ζ=0.05) 332.9(14.0) 248.4(11.1) 4415.6(9.4) 0.503(0.022) 0.019(0.002) 0.253(0.023) 0.054(0.002)
NOISeq(ζ=0.05) 196.8(11.0) 191.4(10.8) 4494.6(2.5) 0.617(0.022) 0.001(0.001) 0.028(0.013) 0.064(0.002)
SAMSeq(ζ=0.05) 274.3(15.7) 212.1(7.7) 4437.8(10.9) 0.576(0.015) 0.014(0.002) 0.226(0.029) 0.061(0.001)
TSPM(ζ=0.05) 129.9(10.5) 80.1 (8.9) 4450.2(7.1) 0.840(0.018) 0.011(0.002) 0.383(0.046) 0.086(0.002)
  1. #Empirical estimates of the standard deviation were reported in the parentheses
  2. edgeR 1 estimates common dispersion parameter for all tags; edgeR 2 estimats tag-wise dispersion parameters
  3. ζdenotes the false discovery rate