Hi AaronYou can try this code below. Much of this has been compiled from
information out of R vignettes and the RMA Express website (*rma*
express.bmbolstad.com).

Before doing all this you may want to either download and/or install the
correct libraries to read in your chips. After you have done that:
For standard RMA normalization i.e. gene-level data
> library(affy)
> setwd("<your working dir that has the cel files>")
> eset<-justRMA()
You can also do
> data<-ReadAffy()
> eset<-rma(data)
To write out your data
> write.exprs(eset,file="eset.txt")
Get probe level unnormalized intensities of Affy data
> pmdata=log2(pm(data))  # for 2-logged data
> write.table(pmdata,file="my_pm_data.txt",sep="\t")
> data2=exprs(data) # for unlogged data
> write.table(data2,file="my_data.txt",sep="\t")

If you need probe-level intensities (unnormalized) w. corresponding probe
names rather than the probe index numbers as above will provide:
> y=pm(data,geneNames(data)) # for unlogged data
> write.table(y,file="file.txt")
> y2=log2(pm(data,geneNames(data)))  # for 2-logged data
> write.table(y2,file="file2.txt")

If you need normalized but unsummarized probe level intensities i.e.
individual probes' intensities after background correction
> data = ReadAffy()
> my.PM <- apply(pm(data), 2, bg.adjust)
> my.Quan <- normalize.quantiles(my.PM)
> y2=log2(pm(data,geneNames(data)))
> Quan_log<-log2(my.Quan)
> rownames(Quan_log)=rownames(y2)
> colnames(Quan_log)=sampleNames(data)
> write.table(Quan_log,"rma_abatch_norm.txt")
> write.table(Quan_log,"rma_abatch_norm.txt",quote=F,sep="\t")


On Mon, Jan 12, 2009 at 10:17 AM, Skewes,Aaron <ASkewes@mdanderson.org>wrote:

> Hello,
>
> Can anybody advise me on how to get gene-level rma vs. probe-level rma
> using  rma(...) method in the Affy package for the HTHGU133A platform?
>
> Thank You,
> Aaron
>
>
>
>
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