I've Human Exon v2 microarray expression data for 223 people. I think I'm lost on my way to analyse data using different packages, normalization, etc. Would really appreciate your help. Here, I'm using aroma to get FIRMA scores but I get 0 or NULL value in output. I'm working with five .cel files to get some thing up and running.

Code and steps:

library("aroma.affymetrix")
cdf <- AffymetrixCdfFile$byChipType("HuEx-1_0-st-v2")
print(cdf)

cs <- AffymetrixCelSet$byName("celfiles", cdf=cdf) # rawdata in cwd. HuEx-1_0-st-v2 in celfiles # this should match cdf file names too
print(cs)
bc <- RmaBackgroundCorrection(cs) #backgroun
csBC <- process(bc,verbose=verbose)

qn <- QuantileNormalization(csBC, typesToUpdate="pm") #quantile norm
csN <- process(qn, verbose=verbose)

getCdf(csN) ##get CDF infor

plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE) #entrire transcript #for exon-by-exon mergeGroup make FALSE
print(plmTr)

#----alternative splicing for transcript PLM - stage 1
firma <- FirmaModel(plmTr) #The FIRMA analysis only works from the PLM based on transcripts.
fit(firma, verbose=verbose)
fs <- getFirmaScores(firma)
cestrfs <- extractDataFrame(fs, units=1:3, addNames=TRUE) #extract the FIRMA scores -- but Nan

######-------------

#extract the estimates (transcript or probeset) use either - here transcript
#stage 2
cesTr <- getChipEffectSet(plmTr)
trFit <- extractDataFrame(cesTr, units=1:3, addNames=TRUE) # gives 0

I don't know what's wrong here.
For stage 1, FIRMA score per transcript is NAN and estimate for transcript is 0 in stage 2.
Aroma google groups is inactive. :(