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

[Laurent Gautier]

On Thu, Nov 21, 2002 at 05:43:25PM -0000, Stephen Henderson wrote:
> 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)?

The "mas" flavor for bg correction is believed to be the same as the
one in MAS5.0 (and we need to fix the man page "bg.correct" to mention
that).
 
> 
> Does anyone have an opinion about this as compared to the "rma" default
> method for bg.correct?

I think Rafael and Ben have something on the way about that...



L.


> 
> 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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Laurent Gautier			CBS, Building 208, DTU
PhD. Student			DK-2800 Lyngby,Denmark	
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