. Author manuscript; available in PMC: 2013 Jun 1.

Published in final edited form as: Comput Stat Data Anal. 2011 Oct 29;56(6):1748–1756. doi: 10.1016/j.csda.2011.10.020

Table 8.

Observed FDR for the Infinium HumanMethylation27 array when using the raw p-value (Raw), Benjamini & Hochberg (BH), Benjamini & Yekutieli (BY), Holm step down (Holm), the default q-value method which estimates π₀ using a smoothing method (q-smoother), and the q-value method where π₀ is estimated using the bootstrap (q-bootstrap).

Dataset	Raw	BH	BY	Holm	q-smoother	q-bootstrap
Rakyan CD14+	0.698	0.036	0.012	0.006	0.045	0.045
Rakyan CD4	0.452	0.033	0.011	0.004	0.033	0.033
Bell Yoruba 1	0.646	0.052	0.018	0.011	0.060	0.063
Bell Yoruba 2	0.446	0.028	0.013	0.009	0.036	0.035
Liu	0.563	0.030	0.010	0.013	0.030	0.030