localFDR-internal {localFDR}R Documentation

For programmers only. (Not to be called by the users.)

Description

Estimates the probabilities that the alternative hypotheses are true

Usage

find.alternative.prob.threshold(p.values, alternative.prob.threshold=default.alternative.prob.threshold(), marginal.probability= NULL, max.iteration=10, tolerance=cal.marginal.probability.tolerance(default.alternative.prob.threshold()), plot.relative.gain = FALSE, call.browser=FALSE, verbose = TRUE)

Arguments

p.values a vector of p-values that have not been corrected for multiple comparisons. For example, p-values may be calculated from wilcox.test or cor.test for two groups, or from lm for multiple groups. Alternately, permutation-based p-values (achieved significance levels) may be calculated using sample.
alternative.prob.threshold a numeric object, with each element between 0 and 1, that determines the space of possible estimates of the probability that an alternative hypothesis is true: more elements enable more precise estimates at the expense of computation speed.
marginal.probability a known or estimated lower bound on the proportion of p-values that correspond to true alternative hypotheses. The default action is to estimate and print marginal.probability.
max.iteration number of iterations if the estimates of the proportion of true null hypotheses do not converge.
tolerance number specifying how close two successive estimates of the proportion of true null hypotheses are to constitute convergence.
plot.relative.gain if TRUE, the relative desirability will be plotted as a function of the significance level.
call.browser if TRUE, the debugging facilities are used.
verbose if TRUE, additional diagnostics are printed

Details

See the following references for details.

Value

These functions return a minimum probability that an alternative hypothesis can have it to be considered true.

Author(s)

Zahra Montazeri (zahra@math.carleton.ca), David R. Bickel (DavidBickel.66846716@bloglines.com, http://www.davidbickel.com)

References

Bickel, David R. (2004) Error-Rate and Decision-Theoretic Methods of Multiple Testing: Which Genes Have High Objective Probabilities of Differential Expression?, Statistical Applications in Genetics and Molecular Biology 3: Iss. 1, Article 8 . Available on-line at http://www.bepress.com/sagmb/vol3/iss1/art8

Bickel, D. R. (2004) "HighProbability determines which alternative hypotheses are highly probable: Genomic applications include detection of differential gene expression," arXiv.org e-print ID q-bio.QM/0402049. Available on-line at http://arxiv.org/abs/q-bio.QM/0402049

See Also

priorFDR, localFDR, t.test, wilcox.test, cor.test, lm, sample


[Package localFDR version 2.1 Index]