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}}

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.

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}}

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

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}}