Problems with homology packages
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@bosotti-roberta-nervianoms-1085
Last seen 10.2 years ago
Dear list, I'm trying to obtain a list of mouse homologs of human genes present in Affymetrix chips (human hgu133plus2 and mouse 430) following the homology packages Vignette, but I didn't succeded. Here is the code and the error messages I got. I'm using R-2.1.1 and Bioconductor 1.6 package. Could you help me? Thanks, Roberta >library("mmuhomology") >subset(mmuhomologyORGCODE, species_name == "Homo sapiens") Error in subset.matrix(mmuhomologyORGCODE, species_name == "Homo sapiens") : Object "species_name" not found >temp <- mget(mmuhomologyHGID, mmuhomologyDATA) >tempFun <- function(x) { for (i in x) { if (!is.na(i[["homoOrg"]]) && i[["homoOrg"]] == "hsa" && i[["homoPS"]] > 90) { return(i) } } return(NA) } >goodGenes <- sapply(temp, tempFun)> goodGenes <- sapply(temp, tempFun) Error in if (!is.na(i[["homoOrg"]]) && i[["homoOrg"]] == "hsa" && i[["homoPS"]] > : missing value where TRUE/FALSE needed ********************************************************************** ******** DISCLAIMER AND CONFIDENTIAL NOTICE\ \ The information contai...{{dropped}}
hgu133plus2 hgu133plus2 • 1.2k views
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@james-w-macdonald-5106
Last seen 8 hours ago
United States
Bosotti, Roberta [Nervianoms] wrote: > Dear list, > > I'm trying to obtain a list of mouse homologs of human genes present in > Affymetrix chips (human hgu133plus2 and mouse 430) following the homology > packages Vignette, but I didn't succeded. Here is the code and the error > messages I got. > I'm using R-2.1.1 and Bioconductor 1.6 package. > Could you help me? > Thanks, Roberta > > >>library("mmuhomology") >>subset(mmuhomologyORGCODE, species_name == "Homo sapiens") > > Error in subset.matrix(mmuhomologyORGCODE, species_name == "Homo sapiens") : > > Object "species_name" not found What version of the mmuhomology package are you using? This works for me. > subset(mmuhomologyORGCODE, species_name =="Homo sapiens") species_name tax_id tla 24 Homo sapiens 9606 hsa > >>temp <- mget(mmuhomologyHGID, mmuhomologyDATA) >>tempFun <- function(x) { > > for (i in x) { > if (!is.na(i[["homoOrg"]]) && i[["homoOrg"]] == > "hsa" && i[["homoPS"]] > 90) { > return(i) > } > } > return(NA) > } > I think you are missing something here. You also have to test for homoType == "B". If homoType == "c", then you will return an NA, which is why your tempFun is erroring out. tempFun <- function(x) { for (i in x) { if (!is.na(i[["homoOrg"]]) && i[["homoOrg"]] == "hsa" && i[["homoType"]] == "B" && i[["homoPS"]] > 90) { return(i) } } return(NA) } HTH, Jim >>goodGenes <- sapply(temp, tempFun)> goodGenes <- sapply(temp, tempFun) > > Error in if (!is.na(i[["homoOrg"]]) && i[["homoOrg"]] == "hsa" && > i[["homoPS"]] > : > missing value where TRUE/FALSE needed > > > > > ******************************************************************** ********** > DISCLAIMER AND CONFIDENTIAL NOTICE\ \ The information contai...{{dropped}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive 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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@bosotti-roberta-nervianoms-1085
Last seen 10.2 years ago
Dear Jim, thanks for your help, it's working now. I have a further question, once I got the HomologeneIDs, I'd like to get the Accession numbers for both human and mouse. The HomologeneIDs that I find do not match with the ones I can retrieve from the NCBI Homologene home page, possibly because they are based on two different release. Do you know where I could find HomoloGene and LocusLink database release that where used in the package? Thanks again for your kind support, Roberta -----Original Message----- From: James W. MacDonald [mailto:jmacdon@med.umich.edu] Sent: Monday, July 04, 2005 2:07 PM To: Bosotti, Roberta [Nervianoms] Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Problems with homology packages Bosotti, Roberta [Nervianoms] wrote: > Dear list, > > I'm trying to obtain a list of mouse homologs of human genes present in > Affymetrix chips (human hgu133plus2 and mouse 430) following the homology > packages Vignette, but I didn't succeded. Here is the code and the error > messages I got. > I'm using R-2.1.1 and Bioconductor 1.6 package. > Could you help me? > Thanks, Roberta > > >>library("mmuhomology") >>subset(mmuhomologyORGCODE, species_name == "Homo sapiens") > > Error in subset.matrix(mmuhomologyORGCODE, species_name == "Homo sapiens") : > > Object "species_name" not found What version of the mmuhomology package are you using? This works for me. > subset(mmuhomologyORGCODE, species_name =="Homo sapiens") species_name tax_id tla 24 Homo sapiens 9606 hsa > >>temp <- mget(mmuhomologyHGID, mmuhomologyDATA) >>tempFun <- function(x) { > > for (i in x) { > if (!is.na(i[["homoOrg"]]) && i[["homoOrg"]] == > "hsa" && i[["homoPS"]] > 90) { > return(i) > } > } > return(NA) > } > I think you are missing something here. You also have to test for homoType == "B". If homoType == "c", then you will return an NA, which is why your tempFun is erroring out. tempFun <- function(x) { for (i in x) { if (!is.na(i[["homoOrg"]]) && i[["homoOrg"]] == "hsa" && i[["homoType"]] == "B" && i[["homoPS"]] > 90) { return(i) } } return(NA) } HTH, Jim >>goodGenes <- sapply(temp, tempFun)> goodGenes <- sapply(temp, tempFun) > > Error in if (!is.na(i[["homoOrg"]]) && i[["homoOrg"]] == "hsa" && > i[["homoPS"]] > : > missing value where TRUE/FALSE needed > > > > > ********************************************************************** ****** ** > DISCLAIMER AND CONFIDENTIAL NOTICE\ \ The information contai...{{dropped}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive 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. ********************************************************************** ******** DISCLAIMER AND CONFIDENTIAL NOTICE\ \ The information contai...{{dropped}}
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Bosotti, Roberta [Nervianoms] wrote: > Dear Jim, > > thanks for your help, it's working now. > I have a further question, once I got the HomologeneIDs, I'd like to get the > Accession numbers for both human and mouse. > The HomologeneIDs that I find do not match with the ones I can retrieve from > the NCBI Homologene home page, possibly because they are based on two > different release. Do you know where I could find HomoloGene and LocusLink > database release that where used in the package? For the HomoloGene release, see ?mmuhomology. I'm not sure if this was built using LL or Entrez Gene ids. Since it was built on 15 May, I think Entrez Gene ids would have been used, but the URL for HomoloGene in ?mmuhomology points to an old build that seems to use LL ids. Maybe Seth Falcon or Chenwei Lin can comment? Best, Jim > > Thanks again for your kind support, > > Roberta > -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive 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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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 10.2 years ago
Hi Roberta, On 4 Jul 2005, jmacdon at med.umich.edu wrote: >> thanks for your help, it's working now. I have a further question, >> once I got the HomologeneIDs, I'd like to get the Accession numbers >> for both human and mouse. The HomologeneIDs that I find do not >> match with the ones I can retrieve from the NCBI Homologene home >> page, possibly because they are based on two different release. Do >> you know where I could find HomoloGene and LocusLink database >> release that where used in the package? > > For the HomoloGene release, see ?mmuhomology. I'm not sure if this > was built using LL or Entrez Gene ids. Since it was built on 15 May, > I think Entrez Gene ids would have been used, but the URL for > HomoloGene in ?mmuhomology points to an old build that seems to use > LL ids. Maybe Seth Falcon or Chenwei Lin can comment? The homologene data provided by NCBI underwent a significant change prior to the BioC 1.6 release. As part of the change, the homology data for a number of species that were previously included in the data were removed. The meaning of the homologene IDs also changed, I believe. For this release we decided it was best to stick with the homology packages from the previous release --- they were rebuilt for compatibility with R 2.1.x, but if I am remembering the events correctly, the data in the homology packages is identical to what was available in the 1.5 release. Our team _is_ working on an updated set of homology packages that will be made available in the development annotation repository soon. Hope that helps explain what you are seeing. Best, + seth
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@bosotti-roberta-nervianoms-1085
Last seen 10.2 years ago
Hi Seth Yes, it make sense. Thanks for the explanation. Regards, Roberta ---------------------------------------------------------------------- Hi Roberta, On 4 Jul 2005, jmacdon at med.umich.edu wrote: >> thanks for your help, it's working now. I have a further question, >> once I got the HomologeneIDs, I'd like to get the Accession numbers >> for both human and mouse. The HomologeneIDs that I find do not >> match with the ones I can retrieve from the NCBI Homologene home >> page, possibly because they are based on two different release. Do >> you know where I could find HomoloGene and LocusLink database >> release that where used in the package? > > For the HomoloGene release, see ?mmuhomology. I'm not sure if this > was built using LL or Entrez Gene ids. Since it was built on 15 May, > I think Entrez Gene ids would have been used, but the URL for > HomoloGene in ?mmuhomology points to an old build that seems to use > LL ids. Maybe Seth Falcon or Chenwei Lin can comment? The homologene data provided by NCBI underwent a significant change prior to the BioC 1.6 release. As part of the change, the homology data for a number of species that were previously included in the data were removed. The meaning of the homologene IDs also changed, I believe. For this release we decided it was best to stick with the homology packages from the previous release --- they were rebuilt for compatibility with R 2.1.x, but if I am remembering the events correctly, the data in the homology packages is identical to what was available in the 1.5 release. Our team _is_ working on an updated set of homology packages that will be made available in the development annotation repository soon. Hope that helps explain what you are seeing. Best, + seth ********************************************************************** ******** DISCLAIMER AND CONFIDENTIAL NOTICE\ \ The information contai...{{dropped}}

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