| INCA.NormSI {INCATome} | R Documentation |
INCATome Normalisation by Spike In Probes
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"))