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Table 7 Statistical significance between two methods for Datasets 3–38

From: A weighted average difference method for detecting differentially expressed genes from microarray data

a) MAS   Inferior
   WAD AD FC RP modT samT shrinkT ibmT
Superior WAD - 2.1E-07 6.7E-07 2.3E-06 2.2E-02 1.7E-02 2.0E-02 1.8E-01
  AD 1.0E+00 - 8.1E-01 2.9E-04 1.0E+00 1.0E+00 1.0E+00 1.0E+00
  FC 1.0E+00 1.9E-01 - 2.6E-04 1.0E+00 1.0E+00 1.0E+00 1.0E+00
  RP 1.0E+00 1.0E+00 1.0E+00 - 1.0E+00 1.0E+00 1.0E+00 1.0E+00
  modT 9.8E-01 8.6E-04 4.0E-03 1.4E-04 - 4.7E-01 9.0E-01 1.0E+00
  samT 9.8E-01 2.5E-04 2.0E-03 6.6E-05 5.3E-01 - 6.9E-01 1.0E+00
  shrinkT 9.8E-01 4.0E-04 2.2E-03 9.0E-05 1.0E-01 3.1E-01 - 1.0E+00
  ibmT 8.2E-01 4.7E-05 2.6E-04 2.6E-05 2.2E-04 2.3E-03 2.9E-04 -
(b) RMA   Inferior
   WAD AD FC RP modT samT shrinkT ibmT
Superior WAD - 9.8E-01 9.8E-01 8.9E-01 3.0E-01 3.1E-01 2.5E-01 4.4E-01
  AD 2.3E-02 - 4.7E-01 8.3E-02 9.2E-03 1.1E-02 7.2E-03 2.8E-02
  FC 2.4E-02 5.3E-01 - 8.8E-02 1.1E-02 1.3E-02 8.4E-03 3.1E-02
  RP 1.1E-01 9.2E-01 9.1E-01 - 8.4E-02 9.7E-02 6.6E-02 1.7E-01
  modT 7.0E-01 9.9E-01 9.9E-01 9.2E-01 - 5.6E-01 6.5E-02 1.0E+00
  samT 6.9E-01 9.9E-01 9.9E-01 9.0E-01 4.4E-01 - 2.1E-01 8.3E-01
  shrinkT 7.5E-01 9.9E-01 9.9E-01 9.3E-01 9.4E-01 7.9E-01 - 1.0E+00
  ibmT 5.6E-01 9.7E-01 9.7E-01 8.3E-01 3.2E-03 1.7E-01 1.9E-03 -
(c) DFW   Inferior
   WAD AD FC RP modT samT shrinkT ibmT
Superior WAD - 1.0E+00 1.0E+00 1.0E+00 1.3E-01 1.2E-01 4.5E-01 1.6E-01
  AD 2.5E-03 - 1.6E-01 9.6E-01 5.1E-02 4.7E-02 2.1E-01 6.9E-02
  FC 2.6E-03 8.4E-01 - 9.6E-01 5.1E-02 4.7E-02 2.1E-01 6.9E-02
  RP 8.7E-04 4.2E-02 4.1E-02 - 3.0E-02 3.0E-02 1.1E-01 4.4E-02
  modT 8.7E-01 9.5E-01 9.5E-01 9.7E-01 - 8.6E-02 9.9E-01 8.5E-01
  samT 8.8E-01 9.5E-01 9.5E-01 9.7E-01 9.1E-01 - 9.9E-01 1.0E+00
  shrinkT 5.5E-01 7.9E-01 7.9E-01 8.9E-01 6.1E-03 1.0E-02 - 2.6E-02
  ibmT 8.4E-01 9.3E-01 9.3E-01 9.6E-01 1.5E-01 5.2E-04 9.7E-01 -
  1. The p-values between the 36 AUC values from a possibly superior method and those from a possibly inferior method were calculated by a one-tail paired t-test. The null hypothesis is that the mean of the 36 AUC values for one method is the same as that for the other method. There are two p-values for two methods compared. For example, in (a) MAS-preprocessed data, the p-value is 1.8E-01 when the alternative hypothesis is that the mean of the 36 AUC values for WAD is greater than that for ibmT while the p-value is 8.2E-01 when the alternative hypothesis is that the mean of the 36 AUC values for ibmT is greater than that for WAD. Combinations having p < 0.05 are highlighted in bold.