you can use rma to normalize them

library(xtable)
library(affyPLM)
library(GOstats)
library(annotate)
library(genefilter)
library(affycoretools)

>
> rawData <- read.affybatch(filenames=list.celfiles())
> sampleNames(rawData)=
> gsub('\\_\\(HG-U133\\_Plus\\_2\\)','',sampleNames(rawData))
>


> eset <- rma(rawData)
>

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