[BioC] aCGH telling me to run find.hmm.states before merge hmm.states even though I have.

[Dan Du]

Hi Cian,

If you look closely, in the first call, you missed something and you
should always operate on the same object. 

hmm(aCGH) <- find.hmm.states(aCGH)

In your case aCGH.hmm only keeps the returned value of the function, but
the original object aCGH was lost. So the error tells you mergeHmmStates
can not find the $hmm slot of the object. hmm() or hmm.merged() is
merely a setter for some specific slot of the aCGH object.

So please follow the code exactly in the vignette unless you know what
is going on behind the scene. 

HTH,
Dan

On Wed, 2013-09-18 at 12:51 +0100, Cian Murphy wrote:
> I have run find.hmm.states by:
> 
> aCGH.hmm <- find.hmm.states(aCGH) on an aCGH object. That seems to run 
> fine as it displays its processing of each chromosome for every sample. 
> I follow it with
> 
> hmm.merged(aCGH.hmm) <-  mergeHmmStates(aCGH.hmm) as per the manual. 
> This nomenclature looks strange so I tried the more normal
> aCGH.hmm.merged <-  mergeHmmStates(aCGH.hmm)
> 
> However both commands give the error
> 
> Error in mergeHmmStates(aCGH.hmm) :
>    compute the hmm states first using find.hmm.states
> 
> 
> What's going on? Why is it asking me to do something that I have just done?
> 
> Thanks,
> 
> 
> Cian
> 
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