Hi, not out of aroma. Aroma will provide you access to the standard DNAcopy/CBS results (as a data frame). From there you have to take it to GLAD yourself; consult the GLAD documentation on how to use the GLAD *caller* by itself.
/Henrik On Tue, May 31, 2011 at 7:30 AM, Yan Jiao <y.j...@ucl.ac.uk> wrote: > Is there a way to run glad model on CBS model result(segmented result) to > call gain/loss? > How should I adapt the code? > > Many thanks > > Yan > > -----Original Message----- > From: aroma-affymetrix@googlegroups.com > [mailto:aroma-affymetrix@googlegroups.com] On Behalf Of Henrik Bengtsson > Sent: 26 May 2011 13:04 > To: aroma-affymetrix@googlegroups.com > Subject: Re: [aroma.affymetrix] copy number gain /loss > > On Thu, May 26, 2011 at 4:18 AM, Yan Jiao <y.j...@ucl.ac.uk> wrote: >> Yes, I am using CBS model, so the method will be DNAcopy right? > > The CBS model is using the CBS method. The CBS method is implemented > in the DNAcopy package. The CbsModel class of the aroma framework is > just a wrapper using the DNAcopy implementation of CBS. > >> I don't think I could use GLAD, since I'm using windows 64bits machine. > > I didn't know that, but you are correct that GLAD is hard to install > in Windows 64-bit. I haven't managed to do it myself, but then I also > didn't really have to do it. It is probably possible, but it > certainly doesn't work out of the box. > > To go back to your original question: the aroma framework does not > implement CN segmentation/calling method itself - it only provides > wrappers to existing ones - and if it doesn't one can always extract > the CN data and pass it on to a segmentation method of choice. > > If you wish to use CBS, then you have to find a way to call the > segments yourself, because the CBS method does not do it for you (and > hence neither aroma). > > Hope this clarifies it. > > /Henrik > >> >> yan >> >> -----Original Message----- >> From: aroma-affymetrix@googlegroups.com >> [mailto:aroma-affymetrix@googlegroups.com] On Behalf Of Henrik Bengtsson >> Sent: 25 May 2011 21:22 >> To: aroma-affymetrix@googlegroups.com >> Subject: Re: [aroma.affymetrix] copy number gain /loss >> >> Hi, >> >> you don't say which method you are using, but I guess you are using >> CBS (CbsModel). If you use GLAD (GladModel), it will also call >> segments for you. >> >> /Henrik >> >> On Wed, May 25, 2011 at 8:21 AM, Yan Jiao <y.j...@ucl.ac.uk> wrote: >>> Hi >>> >>> >>> >>> Does the AROMA package allow copy-number calling? >>> >>> The output I got is just mean and count, is there a way to get copy number >>> gain/loss information? >>> >>> >>> >>> Many thanks >>> >>> >>> >>> Yan >>> >>> -- >>> 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/ >> >> -- >> 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/ > > -- > 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. 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