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
>
> --
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>
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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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