If I load and normalize some two channel arrays

library(limma)

setwd("/vol04/microarray/vineet_study/run_data2")

files <- dir(pattern="*.txt")

RG <- read.maimages(files=dir(),source="agilent",
columns=list(G="gMeanSignal",Gb="gBGMedianSignal",R="rMeanSignal",Rb="rBGMedianSignal"),
annotation = c("Row", "Col","FeatureNum", "GeneName",
"ControlType","ProbeName"))

targets <- readTargets("/vol04/microarray/vineet_study/targets.txt")

RG<- backgroundCorrect(RG, method="none")

MA <- normalizeWithinArrays(RG, method="loess")

E2.avg <- avereps(MA, ID=MA$genes$ProbeName)

and I want to generate ratios of Cy5/Cy3 and Cy3/Cy5

I could convert my MA back to and RG

E2.avg_RG <- RG.MA(E2.avg)

if I do that it will create two unlogged channels again.

question 1 are the intensities still normalized? which channel is Cy3 and
Cy5?

Would the following generate a log ratio of my normalized data(for the
first 12 samples)?

Cy5Cy3_RvsG  <- log2(E2.avg_RG$R[,1:12]/E2.avg_RG$G[,1:12])

Any advice folks have is appreciated.

Thanks

-Rich

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