Hi all, I am trying to get some information on genes (let's say Entrez IDs) through biomaRt, starting from my AffyIDs. I am using drosophila2 Affymetrix chip. Here's some code: library(biomaRt) mart <- useMart(biomart="ensembl", dataset="dmelanogaster_gene_ensembl") grep("affy",c(listAttributes(mart),listFilters(mart))) grep("drosophila2",c(listAttributes(mart),listFilters(mart))) listAttributes(mart)[1:20,] listFilters(mart)[1:20,] and the output I got is attached. My question is: how can I use biomaRt if there are no affy ID in either Attributes and Filters? Am I looking in the wrong place? I remember using it months ago, and it was working properly... Best, Paolo >> library(biomaRt) >> mart <- useMart(biomart="ensembl", > + dataset="dmelanogaster_gene_ensembl") > > Checking attributes and filters ... ok >> grep("affy",c(listAttributes(mart),listFilters(mart))) > integer(0) >> grep("drosophila2",c(listAttributes(mart),listFilters(mart))) > integer(0) >> listAttributes(mart)[1:20,] > name description > 1 bdgp_insitu_expr Bdgp insitu expr > 2 biotype Biotype > 3 chromosome_name Chromosome Name > 4 dedb Dedb > 5 description Description > 6 embl EMBL (Genbank) ID > 7 end_position Gene End (bp) > 8 ensembl_cDNA_length Ensembl cDNA length > 9 ensembl_CDS_length Ensembl CDS length > 10 ensembl_gene_id Ensembl Gene ID > 11 ensembl_peptide_id Ensembl Peptide ID > 12 ensembl_peptide_length Ensembl Peptide length > 13 ensembl_transcript_id Ensembl Transcript ID > 14 entrezgene EntrezGene ID > 15 evidence_code GO evidence code > 16 external_gene_db Gene DB > 17 external_gene_id Gene name > 18 family Ensembl Family ID > 19 family_description Family Description > 20 feat_chr_end Feature chromosome end (bp) >> listFilters(mart)[1:20,] > name description > 1 band_end <na> > 2 band_start <na> > 3 bdgp_insitu_expr Bdgp insitu expr ID(s) > 4 bdgp_insitu_expr-2 Bdgp insitu expr ID(s) > 5 biol_process <na> > 6 biol_process_evidence_code <na> > 7 biotype Type > 8 cell_component <na> > 9 cell_component_evidence_code <na> > 10 chromosomal_region Chromosome Regions > 11 chromosome_name Chromosome name > 12 dedb Dedb ID(s) > 13 dedb-2 Dedb ID(s) > 14 embl EMBL ID(s) > 15 embl-2 EMBL ID(s) > 16 end Gene End (bp) > 17 ensembl_family Ensembl Family ID(s) > 18 ensembl_gene_id Ensembl Gene ID(s) > 19 ensembl_gene_id-2 Ensembl Gene ID(s) > 20 ensembl_peptide_id Ensembl Peptide ID(s) >> >> sessionInfo() > R version 2.7.0 (2008-04-22) > i686-pc-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDEN TIFICATION=C > > attached base packages: > [1] grid splines tools stats graphics grDevices utils > [8] datasets methods base > > other attached packages: > [1] pvclust_1.2-0 drosophila2cdf_2.2.0 Rgraphviz_1.18.0 > [4] drosophila2.db_2.2.0 affycoretools_1.12.0 annaffy_1.12.0 > [7] KEGG.db_2.2.0 biomaRt_1.14.0 RCurl_0.8-3 > [10] GOstats_2.6.0 Category_2.6.0 RBGL_1.16.0 > [13] GO.db_2.2.0 graph_1.18.0 limma_2.14.0 > [16] hopach_1.14.0 cluster_1.11.10 affyQCReport_1.18.0 > [19] geneplotter_1.18.0 annotate_1.18.0 AnnotationDbi_1.2.0 > [22] RSQLite_0.6-8 DBI_0.2-4 lattice_0.17-6 > [25] RColorBrewer_1.0-2 xtable_1.5-2 simpleaffy_2.16.0 > [28] genefilter_1.20.0 survival_2.34-1 affyPLM_1.16.0 > [31] gcrma_2.12.0 matchprobes_1.12.0 affy_1.18.0 > [34] preprocessCore_1.2.0 affyio_1.8.0 Biobase_2.0.0 > > loaded via a namespace (and not attached): > [1] KernSmooth_2.22-22 XML_1.93-2 >>

Dear Paolo, It looks like the Ensembl team removed (possibly accidentally) that affy filter/attribute from the current release. I would report this to helpdesk at ensembl.org and ask them if they can put this attribute/filter back for the drosophila dataset. For now you could query an archived version e.g. the previous Ensembl 48 release and do your queries against that version of Ensembl. (I checked and 48 contains the affy ids). Connect to Ensembl 48 by: listMarts(archive = TRUE) # to show which archives are available ensembl = useMart("ensembl_mart_48", dataset="dmelanogaster_gene_ensembl",archive=TRUE) Cheers, Steffen ---------------------------------------------------------------------- --------- Steffen Durinck, PhD Division of Biostatistics, University of California, Berkeley & Life Sciences Department, Lawrence Berkeley National Laboratory 1 cyclotron Rd, Berkeley CA, 94720, USA Tel: +1-510-486-5123 ---------------------------------------------------------------------- --------- ----- Original Message ----- From: Paolo Innocenti <paolo.innocenti@ebc.uu.se> Date: Wednesday, May 7, 2008 3:48 am Subject: [BioC] AffyID in biomaRt? To: AAA - Bioconductor <bioconductor at="" stat.math.ethz.ch=""> > Hi all, > > I am trying to get some information on genes (let's say Entrez IDs) > through biomaRt, starting from my AffyIDs. > I am using drosophila2 Affymetrix chip. > Here's some code: > > library(biomaRt) > mart <- useMart(biomart="ensembl", > dataset="dmelanogaster_gene_ensembl") > grep("affy",c(listAttributes(mart),listFilters(mart))) > grep("drosophila2",c(listAttributes(mart),listFilters(mart))) > listAttributes(mart)[1:20,] > listFilters(mart)[1:20,] > > and the output I got is attached. > My question is: how can I use biomaRt if there are no affy ID in > either > Attributes and Filters? Am I looking in the wrong place? I remember > using it months ago, and it was working properly... > > Best, > Paolo > > >> library(biomaRt) > >> mart <- useMart(biomart="ensembl", > > + dataset="dmelanogaster_gene_ensembl") > > > > Checking attributes and filters ... ok > >> grep("affy",c(listAttributes(mart),listFilters(mart))) > > integer(0) > >> grep("drosophila2",c(listAttributes(mart),listFilters(mart))) > > integer(0) > >> listAttributes(mart)[1:20,] > > name description > > 1 bdgp_insitu_expr Bdgp insitu expr > > 2 biotype Biotype > > 3 chromosome_name Chromosome Name > > 4 dedb Dedb > > 5 description Description > > 6 embl EMBL (Genbank) ID > > 7 end_position Gene End (bp) > > 8 ensembl_cDNA_length Ensembl cDNA length > > 9 ensembl_CDS_length Ensembl CDS length > > 10 ensembl_gene_id Ensembl Gene ID > > 11 ensembl_peptide_id Ensembl Peptide ID > > 12 ensembl_peptide_length Ensembl Peptide length > > 13 ensembl_transcript_id Ensembl Transcript ID > > 14 entrezgene EntrezGene ID > > 15 evidence_code GO evidence code > > 16 external_gene_db Gene DB > > 17 external_gene_id Gene name > > 18 family Ensembl Family ID > > 19 family_description Family Description > > 20 feat_chr_end Feature chromosome end (bp) > >> listFilters(mart)[1:20,] > > name description > > 1 band_end <na> > > 2 band_start <na> > > 3 bdgp_insitu_expr Bdgp insitu expr ID(s) > > 4 bdgp_insitu_expr-2 Bdgp insitu expr ID(s) > > 5 biol_process <na> > > 6 biol_process_evidence_code <na> > > 7 biotype Type > > 8 cell_component <na> > > 9 cell_component_evidence_code <na> > > 10 chromosomal_region Chromosome Regions > > 11 chromosome_name Chromosome name > > 12 dedb Dedb ID(s) > > 13 dedb-2 Dedb ID(s) > > 14 embl EMBL ID(s) > > 15 embl-2 EMBL ID(s) > > 16 end Gene End (bp) > > 17 ensembl_family Ensembl Family ID(s) > > 18 ensembl_gene_id Ensembl Gene ID(s) > > 19 ensembl_gene_id-2 Ensembl Gene ID(s) > > 20 ensembl_peptide_id Ensembl Peptide ID(s) > >> > >> sessionInfo() > > R version 2.7.0 (2008-04-22) > > i686-pc-linux-gnu > > > > locale: > > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF- > 8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF- > 8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEAS UREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > > > attached base packages: > > [1] grid splines tools stats graphics grDevices > utils > > [8] datasets methods base > > > > other attached packages: > > [1] pvclust_1.2-0 drosophila2cdf_2.2.0 Rgraphviz_1.18.0 > > > [4] drosophila2.db_2.2.0 affycoretools_1.12.0 annaffy_1.12.0 > > > [7] KEGG.db_2.2.0 biomaRt_1.14.0 RCurl_0.8-3 > > > [10] GOstats_2.6.0 Category_2.6.0 RBGL_1.16.0 > > > [13] GO.db_2.2.0 graph_1.18.0 limma_2.14.0 > > > [16] hopach_1.14.0 cluster_1.11.10 > affyQCReport_1.18.0 > > [19] geneplotter_1.18.0 annotate_1.18.0 > AnnotationDbi_1.2.0 > > [22] RSQLite_0.6-8 DBI_0.2-4 lattice_0.17-6 > > > [25] RColorBrewer_1.0-2 xtable_1.5-2 simpleaffy_2.16.0 > > > [28] genefilter_1.20.0 survival_2.34-1 affyPLM_1.16.0 > > > [31] gcrma_2.12.0 matchprobes_1.12.0 affy_1.18.0 > > > [34] preprocessCore_1.2.0 affyio_1.8.0 Biobase_2.0.0 > > > > > loaded via a namespace (and not attached): > > [1] KernSmooth_2.22-22 XML_1.93-2 > >> > > _______________________________________________ > 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