R help - Mar 2009 - Hi, I'm working with custom slides(Cy5) and worki...

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









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