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/
