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
normalize using spike in controls.

My controls are annotated as CTL-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.
The gal file is also loaded with all the array structure. Each block
contains spike in controls.

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$Gb <- NULL
RG$genes <- readGAL("array_human_mirs.gal")

#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

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