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Jo?o Fadista wrote: > Dear list, > > I would like to know how I can retrieve the chromosome position of each UniGene cluster id using biomaRt package. Here it is my script: > > > library(biomaRt) > >>ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > > Checking attributes and filters ... ok > >>unique_UniGeneCluster <- read.csv(file="C:/CGH_experiment2/unique_UniGeneCluster.txt", header=F, sep = "\t") You probably want to use scan() here instead, so you end up with a vector of characters rather than a data.frame of (probably) factors. Alternatively you could unlist() and as.character() your data.frame, but that's sort of a lot of work to undo what you didn't need to do in the first place ;-D Best, Jim >>a <- getGene(id = unique_UniGeneCluster, type = "unigene", mart = ensembl) >>a > > NULL > >>head(unique_UniGeneCluster) > > V1 > 1 Hs.53454 > 2 Hs.433201 > 3 Hs.519601 > 4 Hs.100299 > 5 Hs.459088 > 6 Hs.514038 > >>class(unique_UniGeneCluster) > > [1] "data.frame" > >>session.Info() > > Error: could not find function "session.Info" > >>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" "utils" "datasets" "methods" "base" > > other attached packages: > sma limma biomaRt RCurl XML > "0.5.15" "2.9.17" "1.8.2" "0.8-0" "1.6-0" > > > > > Med venlig hilsen / Regards > > Jo?o Fadista > Ph.d. studerende / Ph.d. student > > > > AARHUS UNIVERSITET / UNIVERSITY OF AARHUS > Det Jordbrugsvidenskabelige Fakultet / Faculty of Agricultural Sciences > Inst. for Genetik og Bioteknologi / Dept. of Genetics and Biotechnology > Blichers All? 20, P.O. BOX 50 > DK-8830 Tjele > > Tel: +45 8999 1900 > Direct: +45 8999 1900 > Mobile: +45 > E-mail: Joao.Fadista at agrsci.dk <mailto:joao.fadista at="" agrsci.dk=""> > Web: www.agrsci.dk <http: www.agrsci.dk=""/> > ________________________________ > > Tilmeld dig DJF's nyhedsbrev / Subscribe Faculty of Agricultural Sciences Newsletter <http: www.agrsci.dk="" user="" register?lan="dan-DK"> . > > Denne email kan indeholde fortrolig information. Enhver brug eller offentligg?relse af denne email uden skriftlig tilladelse fra DJF er ikke tilladt. Hvis De ikke er den tilt?nkte adressat, bedes De venligst straks underrette DJF samt slette emailen. > > This email may contain information that is confidential. Any use or publication of this email without written permission from Faculty of Agricultural Sciences is not allowed. If you are not the intended recipient, please notify Faculty of Agricultural Sciences immediately and delete this email. > > > > [[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 -- 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.

Dear Joao, Try: a <- getGene(id = unique_UniGeneCluster[,1], type = "unigene", mart = ensembl) Also if you are only interested in the chromosomal positions you might want to use the more general getBM function. Your query would look like this: a = getBM(c("unigene","ensembl_transcript_id","chromosome_name","start_pos ition","end_position"),filters="unigene",values= unique_UniGeneCluster[,1] , mart=ensembl) Best regards, Steffen Jo?o Fadista wrote: > Dear list, > > I would like to know how I can retrieve the chromosome position of each UniGene cluster id using biomaRt package. Here it is my script: > > > library(biomaRt) > >> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") >> > Checking attributes and filters ... ok > >> unique_UniGeneCluster <- read.csv(file="C:/CGH_experiment2/unique_UniGeneCluster.txt", header=F, sep = "\t") >> a <- getGene(id = unique_UniGeneCluster, type = "unigene", mart = ensembl) >> a >> > NULL > >> head(unique_UniGeneCluster) >> > V1 > 1 Hs.53454 > 2 Hs.433201 > 3 Hs.519601 > 4 Hs.100299 > 5 Hs.459088 > 6 Hs.514038 > >> class(unique_UniGeneCluster) >> > [1] "data.frame" > >> session.Info() >> > Error: could not find function "session.Info" > >> 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" "utils" "datasets" "methods" "base" > > other attached packages: > sma limma biomaRt RCurl XML > "0.5.15" "2.9.17" "1.8.2" "0.8-0" "1.6-0" > > > > > Med venlig hilsen / Regards > > Jo?o Fadista > Ph.d. studerende / Ph.d. student > > > > AARHUS UNIVERSITET / UNIVERSITY OF AARHUS > Det Jordbrugsvidenskabelige Fakultet / Faculty of Agricultural Sciences > Inst. for Genetik og Bioteknologi / Dept. of Genetics and Biotechnology > Blichers All? 20, P.O. BOX 50 > DK-8830 Tjele > > Tel: +45 8999 1900 > Direct: +45 8999 1900 > Mobile: +45 > E-mail: Joao.Fadista at agrsci.dk <mailto:joao.fadista at="" agrsci.dk=""> > Web: www.agrsci.dk <http: www.agrsci.dk=""/> > ________________________________ > > Tilmeld dig DJF's nyhedsbrev / Subscribe Faculty of Agricultural Sciences Newsletter <http: www.agrsci.dk="" user="" register?lan="dan-DK"> . > > Denne email kan indeholde fortrolig information. Enhver brug eller offentligg?relse af denne email uden skriftlig tilladelse fra DJF er ikke tilladt. Hvis De ikke er den tilt?nkte adressat, bedes De venligst straks underrette DJF samt slette emailen. > > This email may contain information that is confidential. Any use or publication of this email without written permission from Faculty of Agricultural Sciences is not allowed. If you are not the intended recipient, please notify Faculty of Agricultural Sciences immediately and delete this email. > > > > [[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