Hi, I've just committed aroma.core v1.9.1 to CRAN. Keep an eye on
http://cran.r-project.org/web/packages/aroma.core/ so see when it's available. With that installed, you'll be able to do: seg <- GladModel(..., flavor="daglad"); The default "flavor" is "glad", for backward compatibilities. /Henrik On Mon, Jan 10, 2011 at 5:57 PM, Kai <wangz...@gmail.com> wrote: > Thanks, Henrik. Is there way to configure "aroma.cn" so that it > utilizes the "daglad()" in the GLAD package instead of "glad()"? I > found the "daglad()" more flexible than the original "glad" model. > > Best, > Kai > > > On Jan 6, 3:41 am, Henrik Bengtsson <henrik.bengts...@aroma- > project.org> wrote: >> Hi, >> >> >> >> On Tue, Jan 4, 2011 at 8:00 AM, Kai <wangz...@gmail.com> wrote: >> > Hi Henrik, >> >> > I have a couple of questions for you regarding running the GLAD model >> > in aroma.cn. >> >> > I learned from you previously that, when using the CBS model in aroma, >> > I can set "cbs$.calculateRatios = FALSE" if my CN estimates are >> > already ratioed. So my first question here is whether this also >> > applies to the GLAD model, for example: >> >> > ds = AromaUnitTotalCnBinarySet >> > $byName("dataset,paired",chipType="HumanOmni1-Quad"); >> > glad = GladModel(ds); >> > glad$.calculateRatios = FALSE; >> > fit(glad, chromosomes=c(1:23)); >> >> Yes, this will work also for the GladModel class. >> >> >> >> > Another question I have is that, when calling the "fit" function to >> > run the GLAD model, which underlying function in the GLAD package is >> > being called? Is it possible to pass parameters down to this function >> > through "fit" to fine tune the GLAD model? >> >> Yes, any additional arguments passed to fit() will be passed down to >> the internal segmentation method, which for GladModel is glad() of the >> GLAD package. However, it is better to specify the optional arguments >> when setting up the GladModel, e.g. >> >> glad <- GladModel(ds, bandwidth=5); >> >> From the NEWS [http://cran.r-project.org/web/packages/aroma.core/NEWS] >> of aroma.core (v1.7.5): >> >> o Now fit() for CopyNumberSegmentationModel also passed the optional >> arguments ('...') passed to the constructor function. This makes it >> possible to specify all arguments while initiating the model, e.g. >> sm <- CbsModel(..., min.width=5, alpha=0.05). >> >> /Henrik >> >> >> >> > Many thanks! >> >> > 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 websitehttp://www.aroma-project.org/. >> > To post to this group, send email to aroma-affymetrix@googlegroups.com >> > To unsubscribe and other options, go tohttp://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/
