[BioC] problem to compute copy number with crlmm

[Sören Gröttrup]

Hi Robert,
thanks a lot for your detailed answer. You helped me a lot.
Soeren


> 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