Hello Henrik,
I am using the follwing commands to process my data.
library(aroma.affymetrix)
verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
chipType <- "HuEx-1_0-st-v2"
cdf <- AffymetrixCdfFile$byChipType(chipType, tag="web,v_cdf")
print(cdf)
cs <- AffymetrixCelSet$byName("Sample", cdf=cdf)
print(cs)
setCdf(cs, cdf)
bc <- RmaBackgroundCorrection(cs, tag="web,v_cdf")
csBC <- process(bc,verbose=verbose)
qn <- QuantileNormalization(csBC, typesToUpdate="pm")
print(qn)
csN <- process(qn, verbose=verbose)
plmEx <- ExonRmaPlm(csN, mergeGroups=FALSE)
print(plmEx)
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.
--
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