localFDR-internal {localFDR} | R Documentation |
Estimates the probabilities that the alternative hypotheses are true
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)
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 |
See the following references for details.
These functions return a minimum probability that an alternative hypothesis can have it to be considered true.
Zahra Montazeri (zahra@math.carleton.ca), David R. Bickel (DavidBickel.66846716@bloglines.com, http://www.davidbickel.com)
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
priorFDR
, localFDR
, t.test
, wilcox.test
, cor.test
, lm
, sample