[ensembl-dev] EFG Array Mapping - probesets with same name but a different number of probes on different arrays

[Nathan Johnson]

Currently the code does not support differing sizes for the same probeset across arrays. The default behaviour is to take the largest size.

This tends not to occur with commercial arrays and the warning you are seeing is there as a safe guard, such that the user is aware when non-standard array design is loaded.

Nath




On 13 Sep 2010, at 13:49, Oliver, Gavin wrote:

> Hi all,
>  
> I have just started probe2transcript for 6 custom arrays and the first output I got was a series of messages about probesets with the same name having different numbers of probes on the arrays.
>  
> Now, I know what the message means and I know of the existence of these probesets (they are intentionally created like this).
>  
> Why question is – how will probe2transcript.pl actually treat them?  Can I expect annotation problems for these probesets??
>  
> Best,
>  
> Gavin
>  
>  
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Nathan Johnson
Scientific Programmer
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
Email: njohnson at ebi.ac.uk
TelNo: (+44)1223 492629





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