I am trying to obtain transcript level expression using Aroma.affymetrix 
/FIRMA. I did following steps,

*Creating directories*:
work directory: aromaaffy_test

CDF dir: aromaaffy_test/annotationData/chipTypes/HuEx-1_0-st-v2/ 

Data dir: aromaaffy_test/rawData/GBM/HuEx-1_0-st-v2/

*CFD: * 
(name changed; downloaded from HuEx-1_0-st-v2,coreR2,A20070914,EP.CDF 
[38 MB] Core probesets: 18,708 units/transcript clusters, 284,258 
groups/probesets, and 1,082,385 probes.)

 *.CEL files

R version 3.1.1 (2014-07-10)

Platform: x86_64-apple-darwin13.1.0 (64-bit) 

After setting work directory to aromaaffy_test/


verbose <- Arguments$getVerbose(-8, timestamp=TRUE) 

cdf <- AffymetrixCdfFile$byChipType("HuEx-1_0-st-v2")

cs <- AffymetrixCelSet$byName("GBM", cdf=cdf) 

setCdf(cs, cdf) 

bc <- RmaBackgroundCorrection(cs)

csBC <- process(bc,verbose=verbose) 

qn <- QuantileNormalization(csBC, typesToUpdate="pm") 

csN <- process(qn, verbose=verbose)


plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE)

plmEx <- ExonRmaPlm(csN, mergeGroups=FALSE) 


fit(plmTr, verbose=verbose)
cesTr <- getChipEffectSet(plmTr) 

trFit <- extractDataFrame(cesTr, units=NULL, addNames=TRUE) 

trFit.mat <- extractMatrix(cesTr, units=NULL, addNames=TRUE) 


fit(plmEx, verbose=verbose) 

cesEx <- getChipEffectSet(plmEx) 

exFit <- extractDataFrame(cesEx, units=NULL, addNames=TRUE) 

exFit.mat <- extractMatrix(cesEx, units=NULL, addNames=TRUE) 


firma <- FirmaModel(plmTr) 

fit(firma, verbose=verbose) 

fs <- getFirmaScores(firma)


Getting terminated at:

fit(plmTr, verbose=verbose)

Error Message:
Error in readCel(getPathname(this), indices = idxs, readIntensities = FALSE, 


Argument 'indices' is out of range [1,284622]. 

In addition: Warning message: 

In (ns == 0L) & (nchar(unitNames) == 0L) : 

longer object length is not a multiple of shorter object length

I did the same error earlier, when i used extended CDF's 
Extended + Core probesets: 147,476 units/transcript clusters, 804,085 
groups/probesets, and 3,095,094 probes)

I have following two queries.

Could you let me know where I am doing wrong?

Also, is it possible to get the expression values of the isoforms, 
corresponding to ENSEMBL ID,( i.e. ENSTxxxxxxxxx  format) using this 

Best regards


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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