pava.fdr: Estimate of the FDR and the proportion unchanged genes
In SAGx: Statistical Analysis of the GeneChip

Description Usage Arguments Details Value Author(s) References

Estimates tail area and local false discovery rate using isotonic regression

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

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

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

a list with components

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

Per Broberg

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

SAGx documentation built on Nov. 8, 2020, 8:18 p.m.