Hi list,

I am still wonder about the data, which I analyzed by the limma. I accept
that  I am a biology graduate student, and in the learning stage. I am
analyzing the single color data, which had been generated by Agilent 4x44k
platform. With the help of mailing list and limma users guide, I have done
the following analysis. But logFC gives very high values like 320, 1320 etc.
I don't know how really the fitting is happening. Can I rely on this result.
How should I go about it.
#Reading the data.

> RG<-read.maimages(txt_files, columns = list(G = "gMeanSignal", Gb =
>
"gBGMeanSignal",
R="gMedianSignal",Rb="gBGMedian
>
> Signal"),
> annotation= c("Row", "Col",
> "ProbeUID","ProbeName", "GeneName",))


 Rgene<-backgroundCorrect(RG,method='subtract')

#Considering only G as it is single color experiment.
MA<-normalizeBetweenArrays(Rgene$G,method="quantile")

design <- cbind(norm=1,normvstest=c(1,1,1,1,0,0,0,0))
fit <- lmFit(MA, design)
fit <- eBayes(fit)
topTable(fit, coef="normvstest", adjust="fdr")
-- 

Regards,
Abhilash

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