Dear list,
I have 3 questions about threestep (affyPLM) and expresso (AFFY) functions:

   1. Which type of pm correction does threestep function perform? PMonly?
   2. I would like to preprocess my microarray experiment using the
      following steps within the preprocessing method: GCRMA as
      background correction, INVARIANTSET as normalization, PMONLY as pm
      correction and TUKEY-BIWEIGHT (MAS) as summarization procedure. Is
      there any function which I can use to perform it? As far as I
      know, expresso hasn't got GCRMA as background correction and
      threestep function  hasn't got INVARIANTSET as normalization
      procedure. Any tips?
   3. If I want to perform MAS preprocessing using expresso, I think I
      should do it like this:

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

    This is done this way because Affymetrix performs the normalization
    step after summarization. What about if I want to perform NO
    background correction, INVARIANTSET as normalization, MAS as pm
    correction and MAS as summarization? Is it like this?
       eset<- expresso(data, bgcorrect.method = "mas", pmcorrect.method
    = "mas", normalize.method="invariantset" summary.method = "mas")
       exprs(eset)<-log2(exprs(eset))

Thanks in advance,
Javier


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