function_limma {AWFisher} | R Documentation

## use limma function to get pvalue

### Description

use limma function to get pvalue

### Usage

    function_limma(astudy)

### Arguments

`astudy` | A list contains a data matrix and a vector of group label

### Details

use limma function to get pvalue

### Value

A list of pvalue and effect size

### Author(s)

Zhiguang Huo

### Examples

    N0 = 10
    G <- 1000
    GDEp <- 50
    GDEn <- 50

    set.seed(15213)

    astudy <- matrix(rnorm(N0*2*G),nrow=G,ncol=N0*2)
    ControlLabel <- 1:N0
    caseLabel <- (N0 + 1):(2*N0)

    astudy[1:GDEp,caseLabel] <- astudy[1:GDEp,caseLabel] + 2
    astudy[1:GDEp + GDEn,caseLabel] <- astudy[1:GDEp,caseLabel] - 2

    alabel <- c(rep(0,length(ControlLabel)),rep(1,length(caseLabel)))
    Study <- list(data=astudy, label=alabel)

    result <- function_limma(Study)
    fdr <- p.adjust(result$pvalue)
    sum(fdr<=0.05)

[Package AWFisher version 1.0.1 Index]