draw.DEnumber: A function to plot the number of DE genes against FDR...

In MetaDE: MetaDE: Microarray meta-analysis for differentially expressed gene detection

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:

figure

p-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).

See Also

count.DEnumber

Examples

#---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)

MetaDE documentation built on May 29, 2017, 9 a.m.