[BioC] gcRMA and normalization

[Ariel Chernomoretz]

Dear Claudio

If you type 

> gcrma

in your R prompt you will see the code of the gcrma wrapper function.

Note that in the last line there is a call to 	the 'rma' function. You just 
need to add as an option 'normalize=FALSE' there.

So you can just copy and paste the code into a text editor. Rename the 
function (for instance: mygcrma),  modify the last line as I told you, and 
source it into R.

Ariel./




On August 30, 2005 04:21 am, 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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Ariel Chernomoretz, Ph.D.
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