FindFpr

A vector of p values, one for each gene, with length m

pvalue

A vector of indices that the corresponding gene are true positive

A vector of integers ranging from 1 to m , length of retrieved
 gene list

topk

Given a vector of sizes of retrieved genes, for each size k, select
 the top k genes with smallest p values and compute the false positive rate from
 the retrieved genes and the true positive genes.

misc

These functions take a gene expression value matrix, a
primary covariate vector, an additional known covariates
matrix.  A two stage analysis is applied to counter the effects
of latent variables on the rankings of hypotheses.  The
estimation and adjustment of latent effects are proposed by
Sun, Zhang and Owen (2011).  "leapp" is developed in the
context of microarray experiments, but may be used as a general
tool for high throughput data sets where dependence may be
involved.

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FindFpr: Compute the false positive rate at given sizes of retrieved genes

Description

Usage

Arguments

Value