[BioC] initializing DirichletMultinomial::dmn

[Martin Morgan]

On 07/10/2014 02:45 PM, Charles Berry wrote:
>
> I'd like to be able to specify the starting 'centers' for dmn().
>
> Details:
>
> IIUC DirichletMultinomial::dmn(count, k) will initialize the EM algorithm
> using a kmeans heuristic for selecting the starting point. Replicate runs on
> the same data can yield stark differences in the result.
>
> I have a dataset in which it seems that naively chosen random starting
> centers rarely minimize a goodness-of-fit criterion.
>
> The release version of dmn() does not currently allow for specification of
> starting values. I wonder if there are plans to extend it in this manner?

I'll look into this, thanks for the suggestion. Is there a more general issue 
that makes the random centers choice a poor one? And presumably setting the 
random number seed allows for replication (I think that's a 'this is the way it 
should work' rather than a statement of fact...).

Martin

>
> Best,
>
> Chuck
>
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