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Table 1 Evaluation of embedded signal levels with two signal normalizations

From: Generation of Gene Ontology benchmark datasets with various types of positive signal

    selected percentiles
M.T. meth. Signal
Classes
  0 5 25 50 75 95 100
Holm 5 uncorr. 2.54E-05 2.01E-05 1.59E-05 9.99E-06 5.8E-06 4.73E-06 4.26E-06
Holm 10 corrected 0.0556 0.044 0.0348 0.0219 0.0127 0.0104 0.0093
Holm 5 uncorr. 2.54E-05 2E-05 1.58E-05 9.99E-06 5.58E-06 4.73E-06 4.18E-06
Holm 10 corrected 0.0555 0.0437 0.0346 0.0218 0.0122 0.0103 0.0091
FDR 5 uncorr. 0.000124 0.000107 8.69E-05 5.38E-05 4.04E-05 2.75E-05 0.000021
FDR 10 corrected 0.054 0.0481 0.044 0.0281 0.0191 0.0114 0.0093
FDR 5 uncorr. 0.000246 0.000219 0.0002 0.000128 8.69E-05 0.000052 4.23E-05
FDR 10 corrected 0.0547 0.0468 0.0382 0.0236 0.0177 0.0121 0.0092
  1. Table shows the summary of results with reported percentiles. Signal generation is tested with 5 and 10 positive classes and with signal normalizations that use Holm's method and FDR. Note that 5 percentile limit and 95 percentile limit stay within the required 0.01-0.05 range. Minimum and maximum show deviation from the signal range but the deviation is always only appr. 10% of the allowed signal.