INCA.NormSI: INCATome Normalisation by Spike In Probes

In INCATome: Internal Control Analysis of Translatome Studies by Microarrays

Description

Performs the INCATome normalisation using invariance of Spike In probes for microarray data.

Usage

INCA.NormSI(x, SpikeFile, wcol, base = 2, mva = TRUE, highlight = NULL)

Arguments

x	an RGList object
SpikeFile	a data.frame specifying the Spike In probe names 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.
wcol	an integer specifying the number of the column where Gene Names can be found in the gene annotation table.
base	an integer specifying the log base. Default is 2.
mva	logical, TRUE to plot MA plots before and after normalisation for each array.
highlight	a character vector specifying a set of genes of interest. These will be highlighted in the graphical representations.

Value

A new RGList object containing the normalised array data. Additionally, if mva is TRUE, MA plots before and after normalisations will be generated for each arrays.

Examples

#Load the INCATome Dataset
data(INCATomeData)
attach(INCATomeData)
dc=INCA.NormSI(RGdataBG,sdata,8,highlight=c("ACTB","PABPC1"))

INCATome documentation built on May 2, 2019, 2:38 a.m.