Yes, the process is basically the same; replace AromaUnitTotalCnBinaryFile with AromaUnitFracBCnBinaryFile. Put the TCN and the BAF data files in the same directory. The BAF files should have the same name as the TCN files but with an *,fracB.asb suffix. The use of AromaUnitFracBCnBinaryFile is mentioned in for instance http://aroma-project.org/vignettes/tumorboost-highlevel
/Henrik On Thu, Jan 12, 2012 at 3:03 PM, Kai <wangz...@gmail.com> wrote: > Hi Henrik, > > I have a set of SNP array data on the Illumina Omni1-Quad platform which we > use for inferring copy numbers. I can process these data using GenomeStudio > and export the LRR and BAF data. Previously I've created a custom chipType > in aroma for this array and loaded the LRR data into an > AromaUnitTotalCnBinary set, following the instructions you provided in > vignette: http://www.aroma-project.org/node/88. I was wondering whether I > can also create binary data files in aroma that store the BAF data? My > intent is to get allele-specific copy number estimates and perform paired > PSCBS segmentation as you recently introduced in vignette: > http://www.aroma-project.org/vignettes/PairedPSCBS-lowlevel. > > Thank you very much for your help. > > Best, > Kai > > -- > 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/ -- 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/
