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

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)

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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