SAGx (version 1.46.0)

pava.fdr: 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

Value

• a list with components
• pava.fdr
  estimate of the FDR
• p0
  estimate of p0
• pava.local.fdr
  estimate of the local fdr

Details

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

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