PAA (version 1.7.1)

plotMAPlots: 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').

Value

No value is returned.

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.

Examples

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