Hi Kai. On Tue, Apr 12, 2011 at 3:44 PM, Kai <wangz...@gmail.com> wrote: > Hi Henrik, > > I was very confused by the difference between > "AromaUnitTotalCnBinarySet" and "CnChipEffectSet". I noticed that the > latest CRMAv2 method generates "AromaUnitTotalCnBinarySet", not > "CnChipEffectSet" any more. Are they compatible with each other?
You are referring to doCRMAv2(). Yes, that returns a AromaUnitTotalCnBinarySet, which is contains the total CNs estimates available in the CnChipEffectSet. An AromaUnitTotalCnBinarySet holds CN data that is independent of technology whereas a CnChipEffectSet only holds Affymetrix CN data. In our effort of generalizing part of the Aroma framework to other technologies we have developed the AromaUnitTotalCnBinarySet class (and it's accompanied technology-independent file format). The downstream segmentation methods recognizes both types, e.g. CbsModel(). When using doCRMAv2(), you can still access the CnChipEffectSet, or any other intermediate data sets, by doing res <- doCRMAv2(..., drop=FALSE). Then 'res' will be a named list structure of all datasets and models used in the pipeline. The doCRMAv1(), doRMA() and doGCRMA() methods support the 'drop' argument (which defaults to drop=TRUE). > > Another confusion I have is the difference between > "calculateBaseline()" and "getAverageFile()". I am trying to process a > set of Hapmap samples and use their pooled average as a general copy > number reference. So which function should I use? I'll answer this in a separate thread. /Henrik > > Thank you very much. > > 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/
