
On Nov 12, 2009, at 6:00 AM, bioconductor-request@stat.math.ethz.ch  
wrote:

> Message: 4
> Date: Wed, 11 Nov 2009 14:23:31 +0100 (CET)
> From: S?ren Gr?ttrup <soerengroettrup@uni-muenster.de>
> Subject: Re: [BioC] problem to compute copy number with crlmm
> To: <bioconductor@stat.math.ethz.ch>
> Message-ID:
>        <permail-20091111132331f0889e8400005b79-sgroe_01@message-id.uni-muenster.de 
> >
>
> Content-Type: text/plain; charset=iso-8859-1
>
> Thanks for the fast answer. I will install the new version as soon as
> possible.
>
> I have 12 samples available. But some of them contain the same data  
> because I
> copied them to get more then 10 samples. Hope that's not a problem.
>
> S?ren

Hi S?ren,

Yes, this would explain zeros for the within-genotype variance and the  
resulting error you observed.  CRLMM does not pre-compute the  
parameters needed to estimate copy number because of large batch  
effects.    The best solution would be to run these samples with other  
samples that were processed at a similar time in the same lab. If this  
is not possible, an alternative is to obtain a collection of samples  
processed at a different time in a different lab (such as hapmap).   
The problem with this latter approach is that apparent alterations in  
copy number estimates likely reflect batch differences.  The genotype  
estimates provided by crlmm are much more robust to batch effects than  
copy number estimates -- running crlmm on just your samples is  
perfectly fine.  Getting reliable estimates of copy number for a very  
small number of samples is a challenging problem.

Rob


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