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

[Benilton Carvalho]

library(oligo)
data = read.celfiles(list.celfiles(data_dir, full=T))
idx = oligo:::getFidProbeset(data)
theProbes = exprs(data[idx,])
bgData = rma.background.correct(theProbes)
normData = normalize.quantiles(log2(bgData))

On Dec 26, 2009, at 5:56 PM, Peng Yu wrote:

> library(oligo)
> data<-read.celfiles(list.celfiles(data_dir, full.names=TRUE))
> pm(data)
> 
> Do you mean the above commands? If that is the case, you misunderstood
> me. I don't need the original probe values.
> 
> 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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>> 
>> 
> 
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