[R] [BioC] How to do RMA without summary to probeset level?

[Peng Yu]

I think that you misunderstood me.

As far as I know, RMA does three things: background correction,
quantile normalization, and summary from probes to probesets. I want
the probe values after background correction and quantile
normalization but before the summary.

On Sat, Dec 26, 2009 at 12:07 PM, Benilton Carvalho <bcarvalh at jhsph.edu> wrote:
> pm(data)
>
> b
>
> On Dec 26, 2009, at 2:21 PM, Peng Yu wrote:
>
>> I use the following code to do RMA. I'm wondering how get the probe
>> level values before the summary to the probeset level values.
>>
>> library(oligo)
>> data<-read.celfiles(list.celfiles(data_dir, full.names=TRUE))
>> eset<-rma(data)
>> write.exprs(eset, file='output_file_name', sep="\t")
>>
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>
>