FDRsamplesize2 (version 0.2.0)

fdr.power.alpha: Compute FDR for given p-value threshold, average power and proportion of tests with a true null

Description

Compute the FDR for given values of the p-value threshold alpha, average power, and proportion pi0 of tests with a true null hypothesis.

Usage

fdr.power.alpha(alpha, pwr, pi0, method = "HH")

Value

FDR

Arguments

alpha

p-value threshold (vector)

pwr

average power

pi0

actual proportion of tests with a true null hypothesis

method

method to estimate proportion pi0 of tests with true null, including: "HH" (p-value histogram height), "HM" (p-value histogram mean), "BH" (Benjamini & Hochberg 1995), "Jung" (Jung 2005)

References

Pounds S and Cheng C, "Sample size determination for the false discovery rate." Bioinformatics 21.23 (2005): 4263-4271.

Gadbury GL, et al. (2004) Power and sample size estimation in high dimensional biology. Statistical Methods in Medical Research 13(4):325-38.

Jung,Sin-Ho."Sample size for FDR-control in microarray data analysis." Bioinformatics 21.14 (2005): 3097-3104.

Ni Y, Seffernick A, Onar-Thomas A, Pounds S. "Computing Power and Sample Size for the False Discovery Rate in Multiple Applications", Manuscript.

Examples

alpha = 1:100/1000;
pwr = rep(0.8,length(alpha));
pi0 = 0.95;
fdr.power.alpha(alpha,pwr,pi0,method="HH")