Hello Henrik,

I am using the follwing commands to process my data.

 verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
 chipType <- "HuEx-1_0-st-v2"
cdf <- AffymetrixCdfFile$byChipType(chipType, tag="web,v_cdf")
cs <- AffymetrixCelSet$byName("Sample", cdf=cdf)
setCdf(cs, cdf)
bc <- RmaBackgroundCorrection(cs, tag="web,v_cdf")
csBC <- process(bc,verbose=verbose)
qn <- QuantileNormalization(csBC, typesToUpdate="pm")
csN <- process(qn, verbose=verbose)
plmEx <- ExonRmaPlm(csN, mergeGroups=FALSE)
fit(plmEx, verbose=verbose)
cesEx <- getChipEffectSet(plmEx)
trFit <- extractDataFrame(cesEx, addNames=TRUE)

My question: the resulting data frame (trFit) has values in regular
scale(same scale as intensity values in .cel files). I expected them
to be in log2 scale. Did i miss a step or we get the values only in
the regular scale.

When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.

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