Diagnostic plots for evaluation of background effects and dye bias effects on different percentiles

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Description

For each probe type, and for each sample, several percentiles are plotted against background intensity, and also against dye bias.

Usage

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quantilePlots(quantiles,backgroundInfo,designInfo,percentilesI=NULL,percentilesII=NULL)

Arguments

quantiles

A list containing three matrices. list$green, list$red and list$II must contain respectively the matrices of percentiles obtained from a betaMatrix for the Type I Green probes, Type I Red probes and Type II probes. See getQuantiles.

designInfo

designInfo matrix returned by getDesignInfo

backgroundInfo

"backgroundInfo" matrix returned by getBackground

percentilesI

List of percentiles to be plotted for Type I probes. Must be a vector of integers from 1 to 100. If set to NULL (by default), the sequence (5,10,...,95) of percentiles is plotted.

percentilesII

List of percentiles to be plotted for Type II probes. Must be a vector of integers from 1 to 100. If set to NULL (by default), the sequence (10,20,...,90) of percentiles is plotted.

Value

Plots are produced and saved as pdf in the current directory.

Author(s)

Jean-Philippe Fortin <jfortin@jhsph.edu>

Examples

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data(greenControlMatrix)
data(redControlMatrix)
data(sampleNames)
data(betaMatrix)
quantiles=getQuantiles(betaMatrix)
backgroundInfo=getBackground(greenControlMatrix, redControlMatrix)
designInfo=getDesignInfo(sampleNames)
quantilePlots(quantiles, backgroundInfo, designInfo)