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Question: biomaRt Error : Affy Human Exon array annotation
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gravatar for Md.Mamunur Rashid
7.4 years ago by
Md.Mamunur Rashid260 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. ?? 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
ADD COMMENTlink modified 7.4 years ago by James W. MacDonald45k • written 7.4 years ago by Md.Mamunur Rashid260
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gravatar for James W. MacDonald
7.4 years ago by
United States
James W. MacDonald45k wrote:
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
ADD COMMENTlink written 7.4 years ago by James W. MacDonald45k
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