Help redarding Limma

Question

[bio]

Hello everyone

I use the following script to normalize the Affy data of GSE23343.

library(affy)

rawdata<-ReadAffy()
PM<-probes(rawdata,which="pm")
AffyInfo<-dimnames(PM)[[1]]
cutpos<-regexpr("\\d+$",AffyInfo,perl=T)
AffyID<-substr(AffyInfo,1,cutpos-1)
probe<-as.numeric(substr(AffyInfo,cutpos,nchar(AffyInfo)))

data.bgc<-bg.correct(rawdata,method="rma")
data.bgc.q<-normalize.AffyBatch.quantiles(data.bgc,type="pmonly")
pm.bgc.q<- probes(data.bgc.q,which="pm")
normalized<-cbind(AffyID,probe,pm.bgc.q)
write.table(normalized,file="NormalR.csv",sep=",",row.names=FALSE, quote=FALSE)

The data is normalized with this method

Can anybody help me to perform the Limma on this normalized data?

[ATpoint]

Please read the limma manual which contains extensive explanation and example code. Feel free then to come back with more specific questions.

[bio]

Can you please check if the script I wrote is right for expression data?

[ATpoint]

Please read the manual, it covers everything you need.