[BioC] homology packages and LocusLink IDs

[Robert Gentleman]

Hi Lynn,
   I am not sure quite what you are asking - the point of that part of  
the vignette is to explain how to map from LocusLink (soon to be Entrez  
Gene) IDs to other things. Typically you have Entrez IDs for other  
reasons - like from an analysis of differential expression, or by  
choosing a particular GO term and finding the associated genes or,  
perhaps mapping an analysis done on one species to another; pretty much  
the list is endless.

    Or are you asking about mapping from Entrez gene ID one to a  
homologous gene, and for that gene you want to get the Entrez Gene ID?  
In that case, right now, you would get the homology environment for the  
appropriate (second) species and use its homologene ID to map to the  
Entrez Gene ID for that species.

I believe that this will be changing in the next release (any day now),  
as Homologene has really changed their data formats and keys, and seem  
to be relying more on Entrez IDs and less on Homologene IDs. They also  
seem to have substantially expanded the information available (and  
contracted the number of species it is available for) we will be trying  
to enhance the packages, but any suggestions or requests would be quite  
welcome.

Regards,
  Robert

On May 13, 2005, at 11:33 AM, Lynn Young wrote:

> Greetings,
>
> In the vignette, "How to use the homology packages" under Task 1, what
> is the recommended method of obtaining the LocusLink IDs of the
> homologous genes?
>
> Sincerely,
> Lynn Young
>
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> Bioconductor at stat.math.ethz.ch
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>
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| Robert Gentleman              phone: (206) 667-7700                    
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| Head, Program in Computational Biology   fax:  (206) 667-1319   |
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