[BioC] homology package question
James W. MacDonald
jmacdon at med.umich.edu
Thu Mar 13 15:00:51 CET 2008
I wasn't sure it needed an update.
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?
> 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.
> > 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.
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
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> Weiwei Shi, Ph.D
> Research Scientist
> GeneGO, Inc.
> "Did you always know?"
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> ---Matrix III
James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
Ann Arbor MI 48109
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