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Gaussian Network

Some values of the empirically estimated performance measures for the tests of differential connectivity of single genes are provided in Tables 2 and 3 of the paper. More detailed tables are given below. The targeted nominal level for the tests are 10%. The number of important genes are 10. The total number of genes is p. In addition to providing values for the performance of the uncorrected and Benjamini-Hochberg procedures, values for the performance of other popular multiplicity corrections are also provided. The proportion of times that the methods could be successfully applied is also provided for these other methods.

p=20 Sensitivity Specificity True Discovery Rate (TDR) True Non-discovery Rate (TNR) Proportion of times method could be applied
n &rho Power none Benjamini-Hochberg locFDR q-value fdrtool fdrtool local none Benjamini-Hochberg locFDR q-value fdrtool fdrtool local none Benjamini-Hochberg locFDR q-value fdrtool fdrtool local none Benjamini-Hochberg locFDR q-value fdrtool fdrtool local locFDR q-value fdrtool fdrtool local
50 0.5 0.334 0.186 0.035 0.038 0.184 0.156 0.092 0.889 0.984 0.966 0.84 0.871 0.934 0.626 0.678 0.528 0.534 0.547 0.583 0.522 0.505 0.501 0.507 0.508 0.507 1 0.906 1 1
200 0.5 0.947 0.48 0.234 0.04 0.479 0.52 0.362 0.838 0.935 0.967 0.662 0.649 0.826 0.748 0.784 0.547 0.587 0.597 0.676 0.617 0.55 0.502 0.56 0.575 0.564 0.991 0.756 1 0.995
50 0.6 0.318 0.184 0.034 0.037 0.184 0.181 0.104 0.876 0.983 0.968 0.837 0.848 0.92 0.597 0.667 0.535 0.53 0.543 0.563 0.518 0.504 0.501 0.506 0.509 0.506 1 0.897 0.999 0.998
200 0.6 0.962 0.594 0.37 0.041 0.619 0.719 0.543 0.757 0.874 0.961 0.55 0.458 0.717 0.71 0.745 0.514 0.579 0.57 0.658 0.651 0.581 0.501 0.591 0.62 0.611 0.98 0.622 1 0.986
50 0.7 0.375 0.215 0.055 0.036 0.235 0.239 0.14 0.834 0.963 0.967 0.785 0.789 0.884 0.565 0.598 0.523 0.521 0.532 0.546 0.515 0.505 0.501 0.506 0.509 0.507 0.999 0.844 1 0.998
200 0.7 0.99 0.704 0.521 0.06 0.753 0.854 0.687 0.638 0.768 0.954 0.423 0.283 0.583 0.661 0.692 0.562 0.566 0.544 0.622 0.683 0.616 0.503 0.631 0.66 0.651 0.977 0.477 1 0.949
50 0.8 0.385 0.246 0.086 0.036 0.273 0.324 0.202 0.752 0.923 0.966 0.728 0.674 0.801 0.498 0.527 0.512 0.501 0.498 0.503 0.499 0.502 0.5 0.5 0.499 0.501 0.996 0.781 1 0.992
200 0.8 0.997 0.827 0.727 0.086 0.856 0.955 0.829 0.459 0.554 0.939 0.282 0.112 0.431 0.605 0.62 0.584 0.544 0.518 0.593 0.726 0.67 0.507 0.662 0.711 0.716 0.924 0.258 1 0.896
50 0.9 0.455 0.265 0.112 0.036 0.34 0.4 0.247 0.687 0.876 0.963 0.637 0.574 0.731 0.459 0.475 0.49 0.484 0.484 0.478 0.483 0.497 0.5 0.491 0.489 0.492 0.995 0.743 1 0.985
200 0.9 0.999 0.928 0.9 0.093 0.977 0.996 0.918 0.26 0.299 0.894 0.104 0.025 0.3 0.557 0.562 0.469 0.522 0.505 0.567 0.784 0.749 0.497 0.821 0.854 0.784 0.748 0.106 1 0.756


p=100 Sensitivity Specificity True Discovery Rate (TDR) True Non-discovery Rate (TNR) Proportion of times method could be applied
n &rho Power none Benjamini-Hochberg locFDR q-value fdrtool fdrtool local none Benjamini-Hochberg locFDR q-value fdrtool fdrtool local none Benjamini-Hochberg locFDR q-value fdrtool fdrtool local none Benjamini-Hochberg locFDR q-value fdrtool fdrtool local locFDR q-value fdrtool fdrtool local
50 0.5 0.898 0.154 0.017 0.006 0.204 0.221 0.199 0.907 0.989 0.996 0.799 0.786 0.821 0.155 0.146 0.139 0.101 0.103 0.11 0.906 0.901 0.9 0.9 0.901 0.902 1 0.846 1 0.999
200 0.5 0.998 0.225 0.02 0.009 0.126 0.09 0.064 0.895 0.994 0.996 0.893 0.928 0.95 0.193 0.275 0.2 0.116 0.122 0.125 0.912 0.901 0.9 0.902 0.902 0.901 1 0.979 0.998 1
50 0.6 0.951 0.161 0.019 0.008 0.177 0.218 0.199 0.914 0.99 0.996 0.828 0.788 0.82 0.172 0.174 0.167 0.102 0.103 0.109 0.907 0.901 0.9 0.9 0.901 0.902 0.999 0.852 1 1
200 0.6 0.997 0.207 0.021 0.006 0.217 0.169 0.136 0.889 0.991 0.995 0.797 0.845 0.884 0.171 0.198 0.126 0.106 0.108 0.115 0.91 0.901 0.9 0.902 0.901 0.902 0.999 0.938 0.998 1
50 0.7 0.992 0.163 0.021 0.009 0.179 0.217 0.195 0.915 0.988 0.995 0.827 0.791 0.826 0.176 0.165 0.155 0.103 0.103 0.111 0.908 0.901 0.9 0.901 0.901 0.902 0.999 0.851 1 0.995
200 0.7 1 0.18 0.02 0.004 0.238 0.2 0.153 0.87 0.986 0.995 0.774 0.814 0.866 0.133 0.133 0.088 0.105 0.107 0.112 0.905 0.9 0.9 0.901 0.902 0.902 1 0.918 1 0.998
50 0.8 1 0.152 0.012 0.011 0.181 0.17 0.153 0.926 0.995 0.995 0.823 0.835 0.86 0.186 0.213 0.211 0.102 0.103 0.108 0.908 0.901 0.901 0.901 0.901 0.901 1 0.882 1 0.999
200 0.8 1 0.134 0.016 0.005 0.206 0.19 0.147 0.865 0.985 0.996 0.795 0.809 0.853 0.099 0.104 0.103 0.1 0.099 0.1 0.9 0.9 0.9 0.9 0.9 0.9 1 0.897 0.998 1
50 0.9 1 0.14 0.012 0.017 0.166 0.178 0.156 0.925 0.994 0.995 0.839 0.827 0.854 0.171 0.183 0.293 0.103 0.103 0.106 0.906 0.901 0.901 0.901 0.901 0.901 1 0.88 1 1
200 0.9 1 0.09 0.012 0.006 0.233 0.205 0.145 0.842 0.977 0.996 0.755 0.777 0.831 0.06 0.056 0.144 0.095 0.093 0.087 0.893 0.899 0.9 0.899 0.898 0.897 0.999 0.904 1 0.998