pava.fdr {SAGx}R Documentation

Estimate of the FDR and the proportion unchanged genes

Description

Estimates tail area and local false discovery rate using isotonic regression

Usage

pava.fdr(ps = pvalues, p0 = NULL)

Arguments

ps the vector of p-values, e.g. from firstpass
p0 an estimate of the proportion unchanged genes

Details

If p0 = NULL the PRE estimate of p0 is calculated.

Value

a list with components

pava.fdr estimate of the FDR
p0 estimate of p0
pava.local.fdr estimate of the local fdr

Author(s)

Per Broberg

References

Broberg, P : A comparative review of estimates of the proportion unchanged genes and the false discovery rate, BMC Bioinformatics 2005, 5(1):199
Aubert J, Bar-Hen A, Daudin J-J, Robin S: Determination of the differentially expressed genes in microarray experiments using local FDR. BMC Bioinformatics 2004, 6(1):125


[Package SAGx version 1.12.0 Index]