plotNormMethods {PAA} | R Documentation

## Check normalization results with boxplots.

### Description

Draws sample-wise boxplots of raw data and data after all kinds of normalization provided by PAA.

### Usage

    plotNormMethods(elist = NULL, include.rlm=FALSE, controls="internal",
    output.path = NULL)

### Arguments

`elist` | `EListRaw` object containing raw data (mandatory).
`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 a folder for saving the boxplots as tiff files (optional).

### Details

For each normalization approach sample-wise boxplots are created. All boxplots can be saved as high-quality tiff files (when an output path has been specified via the argument `output.path`). The resulting boxplots can be used to compare the results of 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,]
    plotNormMethods(elist=elist)

[Package PAA version 1.20.0 Index]