Hi everyone,
I have a weird situation at the moment, as I am processing my HuEx
chips according to your suggested script and all columns in the
fsScores array contain -processed values. I suppose this is not what
it should look like...
Example:
fsScores[1:8,]
unit group cell control1
control2 control3 sample1 sample 2
1 0.000000 0.000000 0.000000 -0.41742728 0.561465793
0.4043409525 0.007372087 0.3121699
2 0.000000 1.000000 1.000000 0.12625074 -0.069064913
0.2345612082 0.986910881 0.2556821
3 0.000000 1.584963 1.584963 0.37939132 0.818689146
0.3518473601 0.482220926 -0.7406933
4 0.000000 2.000000 2.000000 0.17216439 0.395573096
0.2610864484 -0.100257622 0.2619834
5 0.000000 2.321928 2.321928 0.34054436 -1.823549394
-0.8707103789 -1.531021170 -0.3450005
My code looks like this:
chipType <- "HuEx-1_0-st-v2"
cdf <- AffymetrixCdfFile$byChipType(chipType,
tags="fullR3,A20071112,EP")
cs <- AffymetrixCelSet$byName("all_samples", cdf=cdf)
setCdf(cs, cdf)
# BACKGROUND CORRECTION
bc <- RmaBackgroundCorrection(cs, tag="fullR3")
csBC <- process(bc,verbose=verbose)
# QUANTILE NORMALIZATION
qn <- QuantileNormalization(csBC, typesToUpdate="pm")
csN <- process(qn, verbose=verbose)
# FIT SUMMARY MODEL
plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE)
fit(plmTr, verbose=verbose)
cesTr <- getChipEffectSet(plmTr)
trFit <- extractDataFrame(cesTr, units=NULL, addNames=TRUE)
# FIRMA
firma <- FirmaModel(plmTr)
fit(firma, verbose=verbose)
fs <- getFirmaScores(firma)
fsScores <- log2(extractDataFrame(fs))
Any help is greatly appreciated, many thanks in advance.
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