[BioC] gcRMA and normalization

[Zhijin (Jean) Wu]

The bg.adjust.gcrma function is not available in the previous releases. We
are going to include that in the next release. The devel version has this
function and you can try that. We are testing the devel version now. Just
notice currently the devel version has default "fast=FALSE" unlike the
previous releases. You will need to specify "fast=TRUE" if you want to
stay with the previous default settings.

best,
Jean


On Tue, 30 Aug 2005, claudio.is at libero.it wrote:

> Dear Bio.C,
> 
> I want to use gcrma function, to get expression from a genechip experiment, but I don't want to use any normalization methods.
> 
> I tried to use expresso this way,
> 
> > bgcorrect.methods<-c(bgcorrect.methods,"gcrma")
> > n<-expresso(r, bgcorrect.method="gcrma", normalize.method= FALSE, pmcorrect.method="pmonly", summary.method="medianpolish")
> background correction: gcrma
> normalization: FALSE
> PM/MM correction : pmonly
> expression values: medianpolish
> background correcting...Error in bg.correct(afbatch, method = bgcorrect.method) :
>         Unknown method (cannot find function bg.correct.gcrma )
> 
> but as you can see it didn't works...
> 
> do ou have any other suggestion?
> 
> Claudio Isella
> 
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