[BioC] gcRMA and normalization

[claudio.is@libero.it]

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