draw.DEnumber: A function to plot the number of DE genes against FDR obtained from the Meta-analysis.

Description

draw.DEnumber(result,maxcut,mlty=NULL,mcol=NULL,mlwd=NULL,mpch=NULL,FDR=TRUE) plot the number of DE genes against FDR obtained from the Meta-analysis.

Usage

draw.DEnumber(result,maxcut,mlty=NULL,mcol=NULL,mlwd=NULL,mpch=NULL,FDR=TRUE)

Arguments

result

A p-value matrix or an object file from metaDE.rawdata.pvalue,metaDE.pvalue,metaDE.minMCC, metaDE.ES

FDR

use FDR for cutpoints if true, p-value otherwise

maxcut

The maximum cut point for FDR or P-value

mlty

line type for each line. default is set

mcol

line colour. defaut is set

mlwd

line width for each line. default is set

mpch

symbol for each line. default is set

Value

A figure containing:
figurep-value(or FDR) vs numberof detected genes for individual analysis as well as meta analysis.

References

Li and Tseng (2011) and Lu, Li and Tseng (2009).

Examples

Run this code

#---example 1: Meta analysis of Differentially expressed genes between two classes----------#
label1<-rep(0:1,each=5)
label2<-rep(0:1,each=5)
exp1<-cbind(matrix(rnorm(5*200),200,5),matrix(rnorm(5*200,2),200,5))
exp2<-cbind(matrix(rnorm(5*200),200,5),matrix(rnorm(5*200,1.5),200,5))
x<-list(list(exp1,label1),list(exp2,label2))

# here I used modt to generate p-values. 
DEgene<-ind.analysis(x,ind.method=rep("regt",2),tail="abs",nperm=100)

#--then you can use Fisher's method to combine the above p-values
res<-MetaDE.pvalue(DEgene,meta.method='Fisher')
draw.DEnumber(res,FDR=TRUE,maxcut=0.1)