[BioC] Segmentation Demo - problem in normalization

[Wolfgang Huber]

Dear Krys,

please can you provide

1. a script that allows us to reproduce the error condition you get, and
2. the output of sessionInfo()

Otherwise I am afraid your question is too unspecific to do anything
about it.

 Best wishes
 Wolfgang



Krys Kelly wrote:
> I am trying to run the Segmentation Demo. I have been cutting and pasting
> the commands from the Segmentation Demo document. 
> 
> I get an error during the normalization.  When I run this command:
> 
> xn = normalizeByReference(davidTiling[, isRNA], davidTiling[, isDNA], pm =
> PMind, background = isbg)
> 
> I get the following error message:
> 
> The likelihood optimization did not converge. A likely reason is that the
> normalization parameters are not uniquely identifiable from the provided
> data.
> Possibly, the columns of the data matrix are exactly co-linear or affine
> dependent - please verify the data to make sure there were no mix-ups.
> 
> Please can you help.
> 
> Thanks
> 
> Krys
> 
> 
> Dr Krystyna A Kelly
> University of Cambridge
> Department of Pathology
> Molteno Building, Tennis Court Road
> Cambridge CB2 1QP
> Tel:    01223 333331
> Email: kak28 at cam.ac.uk
> 
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Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber