[BioC] Help needed with aroma.affymetrix package to extract copy-numbers

Christian.Stratowa at vie.boehringer-ingelheim.com Christian.Stratowa at vie.boehringer-ingelheim.com
Mon Feb 25 16:01:21 CET 2008

Dear all,

Using aroma.affymetrix I have fitted a GLAD model and would like to extract
the (relative) copy-numbers.

Following the aroma-affymetrix website I did:
# get cdf
> chiptypes <- c("Mapping250K_Sty", "Mapping250K_Nsp")
> cdf <- AffymetrixCdfFile$fromChipType(chiptypes[1])

# get cel
> name <- "TestSty250K"
> cs <- AffymetrixCelSet$fromName(name, chipType=chiptypes[1])

# correct for allelic cross talk
> acc <- AllelicCrosstalkCalibration(cs)
> csC <- process(acc, verbose=verbose)

# quantile normalization 
> cs.ac <- AffymetrixCelSet$fromName(name, tags="ACC,-XY",
> ac.qn  <- QuantileNormalization(cs.ac)
> csCN <- process(ac.qn, verbose=verbose)

# normalization for sequence effects
> cesNList <- list()
> fln <- FragmentLengthNormalization(ces)
> cesNList[[chiptypes[1]]] <- process(fln, verbose=verbose)
> cesN <- cesNList[[chiptypes[1]]]

# fit GLAD model
> glad <- GladModel(cesNList)
> ce <- ChromosomeExplorer(glad)
> process(ce, verbose=verbose)

Since ChromosomeExplorer can use the copy numbers for display, my question
How can now I extract the raw copy-numbers and the fitted copy-numbers from
the fitted GLAD model "glad"?

This is what I tried w/o success:
> tmp <- getRawCnData(glad, cesNList)
# Exception: Argument 'ceList' contains a non-ChipEffectFile: CnChipEffectSet

What kind of list do I need here?
Is this the correct method to use?

Then I tried to extract the data from the files in directory "gladData":
> tmp <- AffymetrixCelSet$fromName(name, tags="QN,ACC,-XY,RMA,A+B,FLN,-XY",
chipType=chiptypes[1], paths=c("gladData"))
# Exception: No files found:

Interestingly, the files in
"gladData/TestSty250K,QN,ACC,-XY,RMA,A+B,FLN,-XY/Mapping250K_Sty" do exist!
What is the reason for this?

P.S.: I can extract the raw copy-numbers manually as described on the
web-site, but not the fitted (and raw) copy-numbers from glad.

Thank you in advance
Best regards

Christian Stratowa, PhD
Boehringer Ingelheim Austria
Dept NCE Lead Discovery - Bioinformatics
Dr. Boehringergasse 5-11
A-1121 Vienna, Austria
Tel.: ++43-1-80105-2470
Fax: ++43-1-80105-2782
email: christian.stratowa at vie.boehringer-ingelheim.com

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