[BioC] homology package question

[Marc Carlson]

James W. MacDonald wrote:
> 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
>>     
>
>   
The older style homology packages have been deprecated and are on the
way out. I have made some new homology packages with the aim of
addressing questions like this by using inparanoid data instead of NCBIs
homologene stuff. These packages are still brand new, but you are
encouraged to try them out (be sure to read the help files) and let me
know if they meet your needs. These packages are presently in the devel
branch. Please have a look at these packages if you are interested:

hom.Hs.inp.db for mappings to human
hom.Rn.inp.db for mappings to rat
hom.Mm.inp.db for mappings to mouse
hom.Dm.inp.db for mappings to fly
hom.Sc.inp.db for mappings to yeast

Let me know if you have further questions, I hope these will help you.

Marc