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Table 3 Probe sets with significant line*probe terms found by F-like test statistics and appropriate residual permutation procedures and Smyth's moderated F-test statistic

From: Generalized shrinkage F-like statistics for testing an interaction term in gene expression analysis in the presence of heteroscedasticity

Test statistic Restricted permutation? Number of probe sets found True false discovery rate Power
F 2 Yes 124 22.6% 12.4%
F 3 Yes 187 29.4% 17.1%
F Gen No 453 29.5% 41.1%
F Gen-gene No 455 28.8% 41.7%
F Gen-grp No 474 28.9% 43.4%
F Gen Yes 136 24.3% 13.3%
F Gen-gene Yes 122 22.1% 12.2%
F Gen grp Yes 116 21.5% 11.7%
moderatedF - 1 N/A 535 34.1% 75.5%
moderatedF - 2 N/A 813 34.4% 68.8%
  1. The CWER was set to 0.05. Gene-specific cutoff values were obtained from 1,000 permutations. "moderated F-1" and "moderated F-2" represent results from using moderated F statistic without any multiple testing adjustment and setting FDR to 5%.