homology package question

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 10 hours ago

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I may be missing something, but I don't understand the contents of the mmuhomologyLL2HGID and mmuhomologyHGID2LL environments. My understanding is that the former should take an Entrez Gene ID as a key and output a HGID number as a value, and the converse for the latter. I am trying to compare results from an experiment using Human samples to a similar experiment using Mouse samples. It seems to me the most reasonable way to do this is to map the set of significant genes from one experiment to HGIDs and then from HGIDs to Entrez Gene IDs for the second species. However, it appears that all the keys for both of these environments are the same (and are all Entrez Gene IDs), and the values are all the same (Entrez Gene IDs as well). I see this with versions 1.15.13 as well as 1.14.2, for both mmuhomology and hsahomology packages. > get("20863", mmuhomologyHGID2LL) 10090 20863 > get("20863", mmuhomologyLL2HGID) 10090 20863 > all.equal(unlist(as.list(mmuhomologyLL2HGID)), unlist(as.list(mmuhomologyHGID2LL))) [1] TRUE Am I missing something? Also, is there a better way to compare the two experiments that I am overlooking? Best, Jim -- 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

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ADD COMMENT • link updated 17.6 years ago by John Zhang ★ 2.9k • written 17.6 years ago by James W. MacDonald 67k

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rgentleman ★ 5.5k

@rgentleman-7725

Last seen 9.5 years ago

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Looks like a bug - you might want to use Inparanoid - hopefully we will move to that some time in the next six months James MacDonald wrote: > I may be missing something, but I don't understand the contents of the mmuhomologyLL2HGID and mmuhomologyHGID2LL environments. My understanding is that the former should take an Entrez Gene ID as a key and output a HGID number as a value, and the converse for the latter. > > I am trying to compare results from an experiment using Human samples to a similar experiment using Mouse samples. It seems to me the most reasonable way to do this is to map the set of significant genes from one experiment to HGIDs and then from HGIDs to Entrez Gene IDs for the second species. However, it appears that all the keys for both of these environments are the same (and are all Entrez Gene IDs), and the values are all the same (Entrez Gene IDs as well). I see this with versions 1.15.13 as well as 1.14.2, for both mmuhomology and hsahomology packages. > >> get("20863", mmuhomologyHGID2LL) > 10090 > 20863 >> get("20863", mmuhomologyLL2HGID) > 10090 > 20863 > >> all.equal(unlist(as.list(mmuhomologyLL2HGID)), > unlist(as.list(mmuhomologyHGID2LL))) > [1] TRUE > > Am I missing something? Also, is there a better way to compare the two experiments that I am overlooking? > > Best, > > Jim > > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

ADD COMMENT • link 17.6 years ago rgentleman ★ 5.5k

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John Zhang ★ 2.9k

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> >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." I remember they said that the XML version will be the one to use in the future. I tried to parse the XML file quite some time ago and did not get the same set of data as the old one. If this is still true, we may need to re- design/change the package. > >But we don't have time to make the changes for this release. Sorry... > >best > >nianhua > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

ADD COMMENT • link 17.6 years ago John Zhang ★ 2.9k

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marco zucchelli ▴ 320

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ADD COMMENT • link 17.6 years ago marco zucchelli ▴ 320

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Nianhua Li ▴ 870

@nianhua-li-1606

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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. 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

ADD COMMENT • link 17.6 years ago Nianhua Li ▴ 870

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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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

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