[BioC] homology packages and LocusLink IDs

[Lynn Young]

Hi Robert,

Thanks for the response.  Congratulations on your new position!

Yes, my question is once I get a list of homologene IDs back from the 
homology environment, is there a simple way to map them to a gene ID.  
The homoLL example doesn't seem to work.

I can wait for the next release and try again, if you like.

Warmly,
Lynn

On May 14, 2005, at 1:51 PM, Robert Gentleman wrote:

...

    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

Lynn Young, PhD * National Institutes of Health, USA
CIT, MSC 5624; Bethesda, Maryland 20892-5624
Phone: (301) 496-1137 * FAX: (301) 402-4544
E-mail: lynny at mail.nih.gov