Description Usage Arguments Details Value Author(s) References See Also Examples

A function to estimate the proportion `pi0`

of true null hypotheses from a 'FAMTmodel' (see also function "pval.estimate.eta0" in package "fdrtool").

1 2 |

`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.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ```
# 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)
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.