[BioC] Affymetrix expression values using threestep?

[Javier Pérez Florido]

Hi everyone,
I'm trying to get affymetrix expression values using three different 
functions: expresso, mas5 and threestep.

Using expresso:

eset<- expresso(object, bgcorrect.method = "mas", pmcorrect.method = 
"mas", normalize = FALSE, summary.method = "mas")
eset<-affy.scalevalue.exprSet(eset)
exprs(eset)<-log2(exprs(eset))

Using mas5
eset<-mas5(data)
exprs(eset)<-log2(exprs(eset))

But I have no idea how to get into this using threestep. I've tried:

eset<-threestep(data,background.method="MAS",normalize.method="scaling",summary.method="tukey.biweight")

But the results are quite different to the ones given by mas5 and 
expresso (which are exactly the same between them). I know that 
threestep returns log2 values...


Any tips??
Thanks in advance,
Javier