Plots for Meta-analysis of gene expression data.

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Description

Plots for meta-analysis

Usage

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IDRplot(m,CombineExp=1:(length(grep("zSco_Ex",colnames(m)))),colPos="black",colNeg="red",pchPos="*",pchNeg="*",type="b",ylab="IDR",xlab="z threshold",...)
CountPlot(kkk,cols,Score=c("FDR","zSco"),kindof=c("two.sided","pos","neg"),type="b",pch="*",ylab="Number of genes",xlab="FDR threshold",CombineExp=1:((ncol(m)-6)/2-1) ,...)

Arguments

m

result matrix of the function zScores

type

plot parameter

ylab

plot parameter

xlab

plot parameter

pch

plot parameter

colPos

color for positive z scores

colNeg

color for negative z scores

pchPos

symbol for positive z scores

pchNeg

symbol for negative z scores

CombineExp

vector of integer- which experiments should be combined-default:all experiments

kkk

result object of function zScoreFDR

cols

vector of cols, one for each experiment, and one for the combination

Score

should the FDR or the zScore be plotted

kindof

"pos", "neg" or "two.sided"

...

additional plot parameter

Details

IDRplot produces a plot described in Choi et al.

Author(s)

M.Ruschhaupt

References

Choi et al, Combining multiple microarray studies and modeling interstudy variation. Bioinformatics, 2003, i84-i90.