[BioC] [Fwd: Re: using gcrma in expresso]

[echang4 at life.uiuc.edu]

Dear BioConductor users,
I am trying to use the gcrma background subtraction in expresso. I found a
post on the BioConductor archives and tried to repeat it. But I am getting
error "couldn't find function "bgcorrect.methods"
Can someone give me some tips and check my code?

> dat<- ReadAffy(filenames=list.celfiles()) # creates an Affybatch
> library(gcrma)
> bgcorrect.methods <- c(bgcorrect.methods, "gcrma")
> pmcorrect.methods <- c(pmcorrect.methods, "gcrma")
> eset<- expresso(dat, bgcorrect.method="gcrma", normalize.method="qspline",
+ pmcorrect.method="gcrma", summary.method="medianpolish")
background correction: gcrma
normalization: qspline
PM/MM correction : gcrma
expression values: medianpolish
background correcting...Error in bg.correct(afbatch, method =
bgcorrect.method) :
        Unknown method (cannot find function bg.correct.gcrma )

thank you very much,
Edmund Chang