Steffen, Thank you for the information. The new feature you describe of getting both input and output ids returned would be very helpful to me. I am using Windows and there is not yet a Windows binary posted. Could you email me one if you have it built? You will have to change the zip suffix as my email server will not allow those types of attachments. Just change the suffix to MWK, my initials. Thanks, Mark Mark W. Kimpel MD (317) 490-5129 Work, & Mobile (317) 663-0513 Home (no voice mail please) 1-(317)-536-2730 FAX -----Original Message----- From: Steffen Durinck [mailto:durincks@mail.nih.gov] Sent: Friday, January 26, 2007 9:24 AM To: Kimpel, Mark William Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] problem with biomaRt getHomolog function Hi Mark, I think the rat entrezgene id 613226 is a recently added entrezgene id and is not yet available in Ensembl. Ensembl updates every two months and the last update of entrezgene id 613226 appears to be December 26 of 2006. So this might be the reason. Also I would suggest you use the developmental version of biomaRt (biomaRt_1.9.15) to do getHomolog queries. A recent change in the BioMart suite enables the biomaRt package to retrieve both the id you use to query and the ids in the result of the query. Here's an example: rat.entrezgene.ID=c("24842","83502","24205") mouse.mart <- useMart("ensembl","mmusculus_gene_ensembl") rat.mart<- useMart("ensembl", "rnorvegicus_gene_ensembl") mouse.homolog<-getHomolog(id =rat.entrezgene.ID, from.mart = rat.mart,from.type = "entrezgene",to.type="entrezgene", to.mart=mouse.mart) > mouse.homolog V1 V2 1 24842 22059 2 24205 11789 3 24205 NA 4 83502 12550 best, Steffen Kimpel, Mark William wrote: > I am trying to use the getHomolog function of package "biomaRt" to map > rat entrezgene IDs to mouse entrezgene IDs. For every ID I try, I get > NULL as return, even when I know that a mouse mapping exists. > > > > For example, ratID "613226" corresponds to mouse "229706" . > > > > See my code and sessionInfo below. Anyone know what I am doing wrong? > > > > Thanks, Mark > > > > >> require(DBI) >> > > [1] TRUE > > >> require(biomaRt) >> > > [1] TRUE > > > > >> mouse.mart <- useMart("ensembl","mmusculus_gene_ensembl") >> > > Checking attributes and filters ... ok > > > > >> rat.mart<- useMart("ensembl", "rnorvegicus_gene_ensembl") >> > > Checking attributes and filters ... ok > > > > >> rat.entrezgene.ID<-"613226" >> > > >> >> > > >> mouse.homolog<-getHomolog(id =rat.entrezgene.ID, from.mart = rat.mart, >> > from.type = "entrezgene", > > + to.type="entrezgene", to.mart=mouse.mart) > > Warning message: > > getBM returns NULL. in: getHomolog(id = rat.entrezgene.ID, from.mart = > rat.mart, from.type = "entrezgene", > > > > > > >> sessionInfo() >> > > R version 2.4.1 (2006-12-18) > > i386-pc-mingw32 > > > > locale: > > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > > > attached base packages: > > [1] "stats" "graphics" "grDevices" "datasets" "utils" "tools" > "methods" "base" > > > > other attached packages: > > biomaRt RCurl XML DBI RWinEdt limma affy affyio > Biobase > > "1.8.1" "0.8-0" "1.2-0" "0.1-12" "1.7-5" "2.9.1" "1.12.2" "1.2.0" > "1.12.2" > > > > Mark W. Kimpel MD > > > > > > Official Business Address: > > > > Department of Psychiatry > > Indiana University School of Medicine > > PR M116 > > Institute of Psychiatric Research > > 791 Union Drive > > Indianapolis, IN 46202 > > > > Preferred Mailing Address: > > > > 15032 Hunter Court > > Westfield, IN 46074 > > > > (317) 490-5129 Work, & Mobile > > > > (317) 663-0513 Home (no voice mail please) > > 1-(317)-536-2730 FAX > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > -- Steffen Durinck, Ph.D. Oncogenomics Section Pediatric Oncology Branch National Cancer Institute, National Institutes of Health URL: http://home.ccr.cancer.gov/oncology/oncogenomics/ Phone: 301-402-8103 Address: Advanced Technology Center, 8717 Grovemont Circle Gaithersburg, MD 20877

Steffen, never mind, I should have looked first, there is no C code in your package and it self-extracted just fine. mark Mark W. Kimpel MD (317) 490-5129 Work, & Mobile (317) 663-0513 Home (no voice mail please) 1-(317)-536-2730 FAX -----Original Message----- From: Steffen Durinck [mailto:durincks@mail.nih.gov] Sent: Friday, January 26, 2007 9:24 AM To: Kimpel, Mark William Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] problem with biomaRt getHomolog function Hi Mark, I think the rat entrezgene id 613226 is a recently added entrezgene id and is not yet available in Ensembl. Ensembl updates every two months and the last update of entrezgene id 613226 appears to be December 26 of 2006. So this might be the reason. Also I would suggest you use the developmental version of biomaRt (biomaRt_1.9.15) to do getHomolog queries. A recent change in the BioMart suite enables the biomaRt package to retrieve both the id you use to query and the ids in the result of the query. Here's an example: rat.entrezgene.ID=c("24842","83502","24205") mouse.mart <- useMart("ensembl","mmusculus_gene_ensembl") rat.mart<- useMart("ensembl", "rnorvegicus_gene_ensembl") mouse.homolog<-getHomolog(id =rat.entrezgene.ID, from.mart = rat.mart,from.type = "entrezgene",to.type="entrezgene", to.mart=mouse.mart) > mouse.homolog V1 V2 1 24842 22059 2 24205 11789 3 24205 NA 4 83502 12550 best, Steffen Kimpel, Mark William wrote: > I am trying to use the getHomolog function of package "biomaRt" to map > rat entrezgene IDs to mouse entrezgene IDs. For every ID I try, I get > NULL as return, even when I know that a mouse mapping exists. > > > > For example, ratID "613226" corresponds to mouse "229706" . > > > > See my code and sessionInfo below. Anyone know what I am doing wrong? > > > > Thanks, Mark > > > > >> require(DBI) >> > > [1] TRUE > > >> require(biomaRt) >> > > [1] TRUE > > > > >> mouse.mart <- useMart("ensembl","mmusculus_gene_ensembl") >> > > Checking attributes and filters ... ok > > > > >> rat.mart<- useMart("ensembl", "rnorvegicus_gene_ensembl") >> > > Checking attributes and filters ... ok > > > > >> rat.entrezgene.ID<-"613226" >> > > >> >> > > >> mouse.homolog<-getHomolog(id =rat.entrezgene.ID, from.mart = rat.mart, >> > from.type = "entrezgene", > > + to.type="entrezgene", to.mart=mouse.mart) > > Warning message: > > getBM returns NULL. in: getHomolog(id = rat.entrezgene.ID, from.mart = > rat.mart, from.type = "entrezgene", > > > > > > >> sessionInfo() >> > > R version 2.4.1 (2006-12-18) > > i386-pc-mingw32 > > > > locale: > > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > > > attached base packages: > > [1] "stats" "graphics" "grDevices" "datasets" "utils" "tools" > "methods" "base" > > > > other attached packages: > > biomaRt RCurl XML DBI RWinEdt limma affy affyio > Biobase > > "1.8.1" "0.8-0" "1.2-0" "0.1-12" "1.7-5" "2.9.1" "1.12.2" "1.2.0" > "1.12.2" > > > > Mark W. Kimpel MD > > > > > > Official Business Address: > > > > Department of Psychiatry > > Indiana University School of Medicine > > PR M116 > > Institute of Psychiatric Research > > 791 Union Drive > > Indianapolis, IN 46202 > > > > Preferred Mailing Address: > > > > 15032 Hunter Court > > Westfield, IN 46074 > > > > (317) 490-5129 Work, & Mobile > > > > (317) 663-0513 Home (no voice mail please) > > 1-(317)-536-2730 FAX > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > -- Steffen Durinck, Ph.D. Oncogenomics Section Pediatric Oncology Branch National Cancer Institute, National Institutes of Health URL: http://home.ccr.cancer.gov/oncology/oncogenomics/ Phone: 301-402-8103 Address: Advanced Technology Center, 8717 Grovemont Circle Gaithersburg, MD 20877