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

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

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%

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%.

ISSN: 1471-2105