INCA.MAPlot {INCATome}

MA Plot for Array data, with optional highlighting of set of genes

Description

Plots MA plot for microarray data and highlights sets of genes and/or SpikeIn probes.

Usage

INCA.MAPlot(x, wcol, spikeIn = TRUE, SpikeFile, prefix = "",
  highlight = NULL)

Arguments

x

an RGList object

wcol

an integer specifying the number of the column where Gene Names can be found in the gene annotation table.

spikeIn

logical, TRUE to highlight SpikeIn Probes. Requires input in SpikeFile.

SpikeFile

a data.frame specifying the Spike In probe names if spikeIn=TRUE in a column called "Probe" and the expected relative amounts for each dye, respectively in a "Cy5" and "Cy3" column. For example, a given probe might be expected in a 3:1 ratio thus column "Cy5" would specify 3 and column "Cy3" would specify 1.

prefix

a character specifying the prefix to be used when saving the plot in a jpeg file.

highlight

a character vector specifying a set of genes of interest to be highlighted in the plot.

Value

Generates jpeg files of MA plots for each arrays.

Examples

#Load the INCATome Dataset
data(INCATomeData)
attach(INCATomeData)
INCA.MAPlot(RGdata,8,spikeIn=TRUE,SpikeFile=sdata, highlight=c("ACTB","PABPC1"))