I had script like this, I have paired samples and using allelic specif copy 
number analysis. 
In this vignette 
(http://aroma-project.org/vignettes/PairedPSCBS-lowlevel/),  manually 
allele-specific copy numbers were estimated. I am thinking whether 
exportTotalCnRatioSet function does the same thing...

 ds  <- doCRMAv2(dataSet, cdf=cdf, plm="AvgCnPlm", 
combineAlleles=combineAlleles, verbose=verbose)
    if(combineAlleles == FALSE){
        dsA <- ds
        ds  <- ds$total
    # tumor-normal match. 
    # Extract the tumors
    dsT <- ds[indexOf(ds, pattern="T")]
    # Extract the normals
    if(paired == TRUE){
        dsN <- ds[indexOf(ds, pattern="N")]
        # We will assume that the names matches
        stopifnot(gsub("T", '',getNames(dsT)) == gsub("N",'', 
        dsN <- ds[indexOf(ds, pattern="N")]
        dsN <- getAverageFile(dsN)

    ## Calculate TCNs
    dsTN    <- exportTotalCnRatioSet(dsT, ref=dsN)


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