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.
>
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>
--
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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