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

[Henrik Bengtsson]

Please post your questions to the aroma.affymetrix mailing list and it
will get answered there.

-Henrik

On Mon, Feb 25, 2008 at 7:01 AM,
<Christian.Stratowa at vie.boehringer-ingelheim.com> wrote:
> 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$fromName(name, tags="ACC,-XY",
>  chipType=chiptypes[1])
>  > ac.qn  <- QuantileNormalization(cs.ac)
>  > csCN <- process(ac.qn, verbose=verbose)
>
>  # normalization for sequence effects
>  > cesNList <- list()
>  > fln <- FragmentLengthNormalization(ces)
>  > cesNList[[chiptypes[1]]] <- process(fln, verbose=verbose)
>  > cesN <- cesNList[[chiptypes[1]]]
>
>  # fit GLAD model
>  > glad <- GladModel(cesNList)
>  > ce <- ChromosomeExplorer(glad)
>  > process(ce, verbose=verbose)
>
>  Since ChromosomeExplorer can use the copy numbers for display, my question
>  is:
>  How can now I extract the raw copy-numbers and the fitted copy-numbers from
>  the fitted GLAD model "glad"?
>
>  This is what I tried w/o success:
>  > tmp <- getRawCnData(glad, cesNList)
>  # Exception: Argument 'ceList' contains a non-ChipEffectFile: CnChipEffectSet
>
>  What kind of list do I need here?
>  Is this the correct method to use?
>
>  Then I tried to extract the data from the files in directory "gladData":
>  > tmp <- AffymetrixCelSet$fromName(name, tags="QN,ACC,-XY,RMA,A+B,FLN,-XY",
>  chipType=chiptypes[1], paths=c("gladData"))
>  # Exception: No files found:
>  gladData/TestSty250K,QN,ACC,-XY,RMA,A+B,FLN,-XY/Mapping250K_Sty
>
>  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
>  Chrstian
>
>  ==============================================
>  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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