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@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..."
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