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

[Benilton Carvalho]

Roumyana Yordanova brought to my attention a mistake on the code suggestion I sent Peng on December 27th.

The correct version is below (please note that normalization is performed on the original scale):

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 = log2(normalize.quantiles(bgData))

As a sanity check, I revisited oligo's code and everything there is as it should.

Thanks a bunch,

b

On Dec 27, 2009, at 11:21 AM, Benilton Carvalho wrote:

> 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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> 
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