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Table 3 Average fraction of false positives: permutation tests.

From: Effects of filtering by Present call on analysis of microarray experiments

  Nominal P-value
  0.050 0.010 0.0010
Unfiltered 0.039 0.007 0.0005
All Absent 0.045 0.008 0.0007
Fraction Present >0 0.035 0.006 0.0005
  1. Permutation of the MAS5 data such that no true positives would be expected were carried out 1000 times. Results shown are the average fraction called significant by the Welch's t-test for selected p-values (0.05, 0.01 and 0.001). Results are for unfiltered data, probe sets called Absent for all samples (37% of the probe sets), and data filtered using fraction Present >0.
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