plotMAPlots {PAA} | R Documentation

## Check normalization results with MA plots.

### Description

Draws MA plots of raw data and data after all kinds of normalization provided by PAA.

### Usage

    plotMAPlots(elist = NULL, idx="all", include.rlm=FALSE, controls="internal",
    output.path = NULL)

### Arguments

`elist` | `EListRaw` object containing raw data (mandatory).
`idx` | integer indicating the column index of the sample for drawing MA plots or the string 'all' for drawing MA plots for all samples (default: all).
`include.rlm` | logical indicating whether RLM normalization should be included (for ProtoArrays only; deafault: FALSE).
`controls` | string indicating the ProtoArray controls for `rlm` normalization (optional). Valid options are `"internal"` (default), `"external"`, `"both"` or a regular expression defining a specific control or a specific set of controls.
`output.path` | string indicating the folder where the tiff files will be saved (mandatory when idx='all').

### Details

When `idx="all"` (default) for each microarray a tiff file containing MA plots for raw data, cyclicoess normalized data, quantile normalized data and vsn normalized data (and, optionally, for ProtoArrays, rlm normalized data) will be created. When `idx` is an integer indicating the column index of a particular sample, MA plots only for this sample will be created. For A and M value computation the artificial median array is used as reference signal. All figures can be saved in `output.path` (mandatory when `idx="all"`). The resulting MA plots can be used to compare the results of the different normalization methods.

### Value

No value is returned.

### Author(s)

Michael Turewicz, michael.turewicz@rub.de

### Examples

    cwd <- system.file(package="PAA")
    load(paste(cwd, "/extdata/Alzheimer.RData", sep=""))
    elist <- elist[elist$genes$Block == 1,]
    plotMAPlots(elist=elist, idx=1)

[Package PAA version 1.28.0 Index]