pi0FAMT | R Documentation |
A function to estimate the proportion pi0
of true null hypotheses from a 'FAMTmodel' (see also function "pval.estimate.eta0" in package "fdrtool").
pi0FAMT(model, method = c("smoother", "density"), diagnostic.plot = FALSE)
model |
'FAMTmodel' object (see |
method |
algorithm used to estimate the proportion of null p-values. Available options are "density" and "smoother" (as described in Friguet and Causeur, 2010) |
diagnostic.plot |
if TRUE the histogram of the p-values with the estimate of |
The quantity pi0
, i.e. the proportion of null hypotheses, is an important parameter when controlling the false discovery rate (FDR). A conservative choice is pi0
= 1 but a choice closer to the true value will increase efficiency and power - see Benjamini and Hochberg (1995, 2000), Black(2004) and Storey (2002) for details.
The function pi0FAMT
provides 2 algorithms to estimate this proportion. The "density" method is based on Langaas et al. (2005)'s approach where the density of p-values f(p) is first estimated considering f as a convex function, and the estimation of pi0
is got for p=1. The "smoother" method uses the smoothing spline approach proposed by Storey and Tibshirani(2003).
pi0
The estimated proportion pi0
of null hypotheses.
Chloe Friguet & David Causeur
Friguet C. and Causeur D. (2010) Estimation of the proportion of true null hypohteses in high-dimensional data under dependence. Submitted.
"density" procedure: Langaas et al (2005) Estimating the proportion of true null hypotheses, with application to DNA microarray data. JRSS. B, 67, 555-572.
"smoother" procedure: Storey, J. D., and R. Tibshirani (2003) Statistical significance for genome-wide experiments. Proc. Nat. Acad. Sci. USA, 100, 9440-9445.
modelFAMT
# Reading 'FAMTdata' data(expression) data(covariates) data(annotations) chicken = as.FAMTdata(expression,covariates,annotations,idcovar=2) # FAMT complete multiple testing procedure model = modelFAMT(chicken,x=c(3,6),test=6,nbf=3) # Estimation of the Proportion of True Null Hypotheses # "density" method ## Not run: pi0FAMT(model,method="density",diagnostic.plot=TRUE) # "smoother" method pi0FAMT(model,method="smoother",diagnostic.plot=TRUE)
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