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",'', getNames(dsN))) }else{ dsN <- ds[indexOf(ds, pattern="N")] dsN <- getAverageFile(dsN) } ## Calculate TCNs dsTN <- exportTotalCnRatioSet(dsT, ref=dsN) Br, C.Y -- -- 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. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.