[BioC] Nomalization using spike-in controls in single channel arrays using limma

[David]

Hi,
I'm working with custom slides(Cy5) and working in the normalization of 
the arrays.
I have three arrays (technical replicates).
I have sucesfully normalized the data using vsn, however i would like to 
compare it to the normalization using spike in controls.

My controls are annotated as control-1 to x and i would like to do 
etiher a normalization by block per array or the mean of all the 
controls per array.

Here is the code:

library(limma)
library(RColorBrewer)
library(vsn)
Cy5 <- "F635 Mean"
Cy5b <- "B635 Mean"
targets <- readTargets("targets.txt")
#My gpr files do only contain 1 channel (Cy5)
RG <- read.maimages( 
targets$FileName,source="genepix",columns=list(R=Cy5,G=Cy5, Rb=Cy5b, 
Gb=Cy5b))
RG$G <- NULL
RG$Gb <- NULL

#Here are my spike in controls for normalization
isSpikeIn <- grep("CTL", RG$genes$Name)

#The vsn normalization works fine
mat <- vsnMatrix(RG$R)

However i would like to normaliza using my spikein controls by block or 
by using the mean of all controls.

Could you help on that ??

thanks,
david