[BioC] homology package question

[James W. MacDonald]

I wasn't sure it needed an update.

library(biomaRt)
?getHomolog

Best,

Jim

Weiwei Shi wrote:
> Dear all,
> 
> I have a question on how to convert Mouse 430 2.0 probe id to entrez 
> gene id (for human). Any update on this old post?
> 
> thanks,
> 
> Weiwei
> 
> On Thu, Apr 19, 2007 at 4:55 AM, James W. MacDonald 
> <jmacdon at med.umich.edu <mailto:jmacdon at med.umich.edu>> wrote:
> 
>     Hi Nianhua,
> 
>     Nianhua Li wrote:
>      > Hi, James,
>      >
>      > The source file of mmuhomology is
>      > ftp://ftp.ncbi.nih.gov/pub/HomoloGene/current/hmlg.ftp (download
>     on 02/28/2007)
>      > and the description is
>      > ftp://ftp.ncbi.nih.gov/pub/HomoloGene/README-old
>      >
>      > According to the description, the 4th and 7th column of hmlg.ftp
>     are Entrez Gene
>      > ID, the 5th and 8th column are internal HomoloGene ID. If you
>     look at the
>      > hmlg.ftp file, even the current one, you can find that the
>     internal HomoloGene
>      > ID is the same as Entrez Gene ID for most of the case. That's why
>      > mmuhomologyHGID2LL and mmuhomologyLL2HGID look identical.
> 
>     Odd. I wonder if they no longer even check to see if the data are
>     correct. I checked several of the IDs, and AFAIK they really are Entrez
>     Gene IDs, and they really are not HomoloGene IDs.
> 
>     Anyway, it's really easy to get the mappings from biomaRt so that might
>     be the direction to point people until we start using an updated source
>     of these data.
> 
>     Best,
> 
>     Jim
> 
> 
>      >
>      > I think we should update the homology packages in the near future
>     to use another
>      > source data because the README file on this site says:
>      >
>      > "The old HomoloGene FTP file formats (hmlg.ftp and hmlg.trip.ftp)
>     are now
>      > deprecated.  They will be produced for the time being, to make the
>      > transition to the new file formats smoother, but will be discontinued
>      > as of Jan. 1, 2007."
>      >
>      > But we don't have time to make the changes for this release. Sorry...
>      >
>      > best
>      >
>      > nianhua
>      >
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> 
> 
>     --
>     James W. MacDonald, M.S.
>     Biostatistician
>     Affymetrix and cDNA Microarray Core
>     University of Michigan Cancer Center
>     1500 E. Medical Center Drive
>     7410 CCGC
>     Ann Arbor MI 48109
>     734-647-5623
> 
> 
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> 
> 
> 
> -- 
> Weiwei Shi, Ph.D
> Research Scientist
> GeneGO, Inc.
> 
> "Did you always know?"
> "No, I did not. But I believed..."
> ---Matrix III

-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623