PAA (version 1.7.1)

plotNormMethods: 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).

Value

No value is returned.

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.

Examples

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