I have an Agilent data set , and i normalized and read it using the code bellow , but my result is different from what the paper claim.

library("limma", lib.loc="~/R/win-library/3.1")
targets<-readTargets("target2.txt",row.names=1,sep="")
targets$Filenames[!file.exists(targets$Filenames)]
x <- read.maimages(targets$Filenames,source="agilent", green.only=TRUE)
y <- backgroundCorrect(x,method="normexp")
NormData<-normalizeBetweenArrays(y,method="quantile")

It is hard for anyone to help you because you give no indication of what the problem is.

You are using a standard limma package normalization method for Agilent microarray data, so no obvious problem there.

What "paper" are you referring to?

What result do you have that is different from theirs, and why is this a problem?

IMPORTANT: Please do not post the same question on more than one mailing list at the same time, as you have done here:

  https://www.biostars.org/p/162449/

This wastes the time of people who might answer you, which is counter-productive as well as impolite.