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));
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?
Many thanks!
Best,
Kai
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