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List:       bioconductor
Subject:    Re: [BioC] affy 1.1 - rma function
From:       Ben Bolstad <bolstad () stat ! berkeley ! edu>
Date:       2002-11-21 16:45:28
Message-ID: 1037897128.1289.8.camel () bmbbox ! yi ! org
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The three step procedure you outline does the same thing with the caveat
that the bg.correct.rma function implements the background correction
step in a slightly different way from the correction carried in the c
code (which duplicates the bg function in affy 1.0 releases).

Ben



> Hi there,
> 
> I have a questions related to what the "rma" function actually does.
> 
> Let assume that I have converted the probe level data stored in the "Data" object \
> to the gene expression values using the following 
> > eset <- rma(Data)
> 
> If I wanted to get the same effect but wanted to do it step by step so that I could \
> save the intermediate AffyBatch objects, then according to my understanding the \
> closest to the above would be the following: 
> > bg.corrected.Data <- bg.correct.rma(Data)
> > norm.Data <- normalize(bg.corrected.Data)
> > eset <- express(norm.Data,bg.correct=F,normalize.method=F,summary.stat=medianpolish)
> > 
> 
> Obviously I won't get exactly the same numbers because "rma" is written in C, so \
> the codes are different, but am I correct in thinking that the above three-step \
> procedure does virtually the same as "rma"? 
> Pawel
> 


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