positionPlots {ARRmNormalization} | R Documentation

## Plots to evalue chip position effects on different percentiles

### Description

For each probe type, and for each sample, deviations from the chip mean are computed for a given percentile. These deviations are plotted against on-chip position.

### Usage

    positionPlots(quantiles,designInfo,percentiles=c(25,50,75))

### 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`
`percentiles` | Vector of percentiles to be plotted. By default, the 25th, 50th and 75th percentiles are plotted. (`percentiles=c(25,50,75)`).

### Value

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

### Author(s)

Jean-Philippe Fortin <jfortin@jhsph.edu>

### Examples

    data(greenControlMatrix)
    data(redControlMatrix)
    data(sampleNames)
    data(betaMatrix)
    quantiles=getQuantiles(betaMatrix)
    backgroundInfo=getBackground(greenControlMatrix, redControlMatrix)
    designInfo=getDesignInfo(sampleNames)
    positionPlots(quantiles, designInfo, percentiles=c(25,50,75))

[Package ARRmNormalization version 1.20.0 Index]