Hi. On Wed, May 9, 2012 at 11:40 AM, Yu Song <[email protected]> wrote: > Dear Henrik, > > I have one question about CBS output.
I'm not 100% sure what you mean by "CBS output", but I guess that you are referring to the "regions.xls" files generated by CbsModel - is that so? There is also the option to get the DNAcopy objects from the binary files (in cbsData/) saved by CbsModel. The latter contains all output returned by the CBS segmentation method (i.e. DNAcopy::segment()). > > Can I transform the CBS result to a standard form like: > > "unitName" "chromosome" "position" patient1 patient2 patient3 So you want to map the CN mean levels estimated by CBS back to each locus. Unfortunately, there is no way to tell CbsModel to output such files. You can always do it manually from DNAcopy objects. It's a tedious programming task though and requires that you understand the structure of the DNAcopy object. Note that this structure is defined by the DNAcopy package (on Bioconductor), and note also that CbsModel of aroma is passing on data to the DNAcopy package and have it do the actual segmentation and return the DNAcopy object. So, in order to understand the DNAcopy object structure, please see its documentation and ask for help on Bioconductor. To get the DNAcopy objects from aroma (which aroma saves to file after running the segmentation), you can do: sm <- CbsModel(ds); fitList <- fit(sm, arrays=3, chromosomes=19, .retResults=TRUE, verbose=TRUE); cbsObject <- fitList[[3]][[19]]; Here 'cbsObject' is an object of class 'DNAcopy'. Searching the aroma.affymetrix mailinglist, you'll find some examples on grabbing the DNAcopy objects this way, e.g. https://groups.google.com/d/topic/aroma-affymetrix/j0kj9N8CY3o/discussion > > So that I that plot the CBS result in the same way like before. This part I don't understand, particularly "the same way like before". If you could provide a better explanation what you wish to achieve, maybe there is a much easier solution to your problem than mapping CN levels back to individual loci. > > I know CBS has one tabulate excel output, but it lists the start and > stop of the position which is hard to transform into the "standard" > output. FYI, the tabular regions.xls files written by CbsModel are simple tab-delimited text files. They have (somewhat misleading) filename extension *.xls just so that they are easy to open in Excel. /Henrik > > > > Thanks a lot. > > -- > Best regards, > Yu Song -- 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 [email protected] To unsubscribe and other options, go to http://www.aroma-project.org/forum/
