[BioC] gcRMA and normalization

claudio.is@libero.it claudio.is at libero.it
Tue Aug 30 10:21:37 CEST 2005

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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