plotNormMethods: Check normalization results with boxplots.

In PAA: PAA (Protein Array Analyzer)

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, [e-mail]

Examples

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

PAA documentation built on Nov. 8, 2020, 8:30 p.m.