Dear List, I have been trying to annotate some Affymetrix Human Exon Array Data using biomaRt. During the summarization I have played around with two cdf Files. 1. HuEx-1_0-st-v2,coreR3,A20071112,EP.CDF (Created by Elizabeth Purdom, UC Berkeley, created - 2007-11-12) unitNames = Affymetrix Transcript cluster IDs unitName groupName unit group cell 1 2315251 2315252 1 1 1 2 2315373 2315374 2 1 3 3 2315554 2315586 3 1 7 ........ Q1. Is there any way to convert this affymetrix transcript cluster Ids ( 2315251 ) to gene symbol, or gene Names using biomaRt.?? If No then what could be the possible way to do it. ?? and 2. HuEx-1_0-st-v2,U-Ensembl49,G-Affy.cdf ( Mark Robinson, Elizabeth Purdom , updated - 2008-04-01 ) unitNames = Ensembl Gene IDs unitName groupName unit group cell 1 ENSG00000000003 4015402 1 1 1 2 ENSG00000000005 3984446 2 1 14 ........ > ensembl = useMart("ensembl") > ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl) > filters = listFilters(ensembl) > attributes = listAttributes(ensembl) r1_2 <- getBM(attributes=c("strand","transcript_start","chromosome_nam e"),filters=c("ens_hs_gene"),values=c("ENSG00000000003"), mart= ensembl) I got the following error.. Error in getBM(attributes = c("strand", "transcript_start", "chromosome_name"), : Query ERROR: caught BioMart::Exception::Database: Error during query execution: Table 'ensembl_mart_58.ox_Ens_Hs_gene__dm' doesn't exist can any body please suggest what could be the possible reason for this.??? Any suggestion is welcome... Thanks in advance regards, Mamun R version 2.11.1 (2010-05-31) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.4.0 loaded via a namespace (and not attached): [1] RCurl_1.4-2 XML_3.1-0

Hi Mamun, On 7/6/2010 8:11 AM, Rashid, Mamunur wrote: > Dear List, > > I have been trying to annotate some Affymetrix Human Exon Array Data > using biomaRt. During the summarization I have played around with two > cdf Files. > > 1. HuEx-1_0-st-v2,coreR3,A20071112,EP.CDF (Created by Elizabeth Purdom, UC Berkeley, created - 2007-11-12) > unitNames = Affymetrix Transcript cluster IDs > > unitName groupName unit group cell > 1 2315251 2315252 1 1 1 > 2 2315373 2315374 2 1 3 > 3 2315554 2315586 3 1 7 > ........ > > Q1. Is there any way to convert this affymetrix transcript cluster Ids ( 2315251 ) to gene symbol, or gene Names > using biomaRt.?? If No then what could be the possible way to do it. ?? > getBM(attributes=c("strand","transcript_start","chromosome_name", "hgnc_symbol"),filters=c("affy_huex_1_0_st_v2"),values=c("2315252"),ma rt) strand transcript_start chromosome_name hgnc_symbol 1 -1 116086 8 2 -1 86649 11 OR4F2P 3 1 180794269 5 OR4F3 4 1 180794269 5 OR4F21 5 1 367640 1 OR4F29 6 -1 621096 1 OR4F16 7 -1 105919 6 8 1 170948694 6 This of course assumes that the groupName above is actually the probeset ID from the chip. > > and > > 2. HuEx-1_0-st-v2,U-Ensembl49,G-Affy.cdf ( Mark Robinson, Elizabeth Purdom , updated - 2008-04-01 ) > unitNames = Ensembl Gene IDs > > unitName groupName unit group cell > 1 ENSG00000000003 4015402 1 1 1 > 2 ENSG00000000005 3984446 2 1 14 > ........ > >> ensembl = useMart("ensembl") >> ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl) >> filters = listFilters(ensembl) >> attributes = listAttributes(ensembl) > > r1_2<- getBM(attributes=c("strand","transcript_start","chromosome_na me"),filters=c("ens_hs_gene"),values=c("ENSG00000000003"), mart= ensembl) > > I got the following error.. > > Error in getBM(attributes = c("strand", "transcript_start", "chromosome_name"), : > Query ERROR: caught BioMart::Exception::Database: Error during query execution: Table 'ensembl_mart_58.ox_Ens_Hs_gene__dm' doesn't exist I think you want 'ensembl_gene_id' as a filter: > r1_2 <- getBM(attributes=c("strand","transcript_start","chromosome_name"), filters=c("ensembl_gene_id"),values=c("ENSG00000000003"), mart) > r1_2 strand transcript_start chromosome_name 1 -1 99883667 X 2 -1 99887538 X 3 -1 99888439 X 4 -1 99884691 X Best, Jim > > can any body please suggest what could be the possible reason for this.??? > Any suggestion is welcome... > > Thanks in advance > > regards, > Mamun > > R version 2.11.1 (2010-05-31) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.4.0 > > loaded via a namespace (and not attached): > [1] RCurl_1.4-2 XML_3.1-0 > > _______________________________________________ > 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 Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues