R help - Dec 2009 - [BioC] How to do RMA without summary to probeset level?

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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>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>

You'll need to use calls to bg.correct and the other functions in
sequence and save the probe values along the way.

See the example in ?normalize.AffyBatch.normalize2Reference in the
caret package.

Also, don't email R help about this. Keep it on the bioC mailing list.

Max

On Sat, Dec 26, 2009 at 2:52 PM, Peng Yu <pengyu.ut at gmail.com>
wrote:
> 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")
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>
>
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> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


-- 

Max