[BioC] bg.correct--which is best?

[Stephen Henderson]

Is the bg.correct method "mas" the same as the newest MAS5.0 one with a
weighted local correction based on grid averages (as I suspect)?

Does anyone have an opinion about this as compared to the "rma" default
method for bg.correct?

Stephen Henderson
WIBR


-----Original Message-----
From: Ben Bolstad [mailto:bolstad@stat.berkeley.edu] 
Sent: Thursday, November 21, 2002 4:45 PM
To: Pawel Herzyk
Cc: bioconductor
Subject: Re: [BioC] affy 1.1 - rma function

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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