Go terms attributes not available on Biomart, ensembl
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chawla ▴ 190
@chawla-4416
Last seen 8.1 years ago
Hi I had also tried ensembl=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl") goterms=getBM(attributes = c("affy_hg_u133a_2", "go_biological_process_id","entrezgene"), filters = "affy_hg_u133a_2", values = data[,1], mart = ensembl) but got the same error I guess its because of change in Go attribute names. Thanks Konika On 18-05-2011 12:00, bioconductor-request at r-project.org wrote: > Send Bioconductor mailing list submissions to > bioconductor at r-project.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://stat.ethz.ch/mailman/listinfo/bioconductor > or, via email, send a message with subject or body 'help' to > bioconductor-request at r-project.org > > You can reach the person managing the list at > bioconductor-owner at r-project.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Bioconductor digest..." > > > Today's Topics: > > 1. Re: Go terms attributes not available on Biomart ensembl > (Steve Lianoglou) > 2. connecting to ensembl (Stefan Kroeger) > 3. Re: Ggallus BS genome package (Namyoung Jung) > 4. SSOAP functions (Michael Gormley) > 5. Re: microRNA hg build? (Marc Carlson) > 6. Re: microRNA hg build? (Jinyan Huang) > 7. arrayQualityMetrics for Affymetrix miRNA chip > (somnath bandyopadhyay) > 8. about limma linear models (Gordon K Smyth) > 9. Re: connecting to ensembl (Hervé Pagès) > 10. Re: Ggallus BS genome package (Hervé Pagès) > 11. Re: alternative to matchprobes (Hervé Pagès) > 12. extract intensity values from AffyBatch (Assa Yeroslaviz) > 13. Re: extract intensity values from AffyBatch (Saurabh Bundela) > 14. Re: extract intensity values from AffyBatch (Assa Yeroslaviz) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 17 May 2011 08:52:28 -0400 > From: Steve Lianoglou<mailinglist.honeypot at="" gmail.com=""> > To: Wolfgang Huber<whuber at="" embl.de=""> > Cc: bioconductor at r-project.org > Subject: Re: [BioC] Go terms attributes not available on Biomart > ensembl > Message-ID:<banlkti=3zfd5hawds=yxpqngxsh97++6=a at="" mail.gmail.com=""> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi, > > There was an email to this list a few days ago about a similar (I > think) problem with GO queries failing. It seems appropriate here(?). > Apparently the identifiers for GO stuffs has changed, see the thread > that starts here: > > https://stat.ethz.ch/pipermail/bioconductor/2011-May/039435.html > > The original poster was querying with something like: > > attributes=c("entrezgene", > "go_cellular_component_id", > "go_cellular_component__dm_name_1006") > > And was getting errors. > > Apparently: > > """the three GO sections have been merged into one. See here for news about > ensembl BioMart changes: > > http://www.ensembl.org/info/website/news/index.html#team-Mart > > These are the names of the attributes you now need to look for: > > > > <query virtualschemaname="default" formatter="TSV" header="0"> uniqueRows = "0" count = "" datasetConfigVersion = "0.6"> > > <dataset name="hsapiens_gene_ensembl" interface="default"> > <attribute name="go_id"/> > <attribute name="name_1006"/> > <attribute name="definition_1006"/> > <attribute name="go_linkage_type"/> > <attribute name="namespace_1003"/> > </dataset> > </query> > > These attribute names correspond to: > > GO Term Accession > GO Term Name > GO Term Definition > GO Term Evidence Code > GO domain > """" > > Hope that helps, > > -steve > > > > On Tue, May 17, 2011 at 2:44 AM, Wolfgang Huber<whuber at="" embl.de=""> wrote: >> Konika >> >> thanks. Your 'sample code' is incomplete. How did you define the object >> 'ensembl'? >> >> ? ? ? ?Best wishes >> ? ? ? ?Wolfgang >> >> >> chawla scripsit 05/15/2011 11:53 PM: >>> Hi >>> I have used BiomaRt to retrieve GO terms for affymetrix probe Ids using >>> mart ensembl. >>> But suddenly all the GO terms attributes have vanished from the list of >>> attributes. >>> I used the sample code to test. >>> >>> ?> affyids = c("202763_at", "209310_s_at", "207500_at") >>> ?> getBM(attributes = c("affy_hg_u133_plus_2", >>> "go_biological_process_id", "chromosome_name", "start_position", >>> + "end_position", "band"), filters = "affy_hg_u133_plus_2", values = >>> affyids, mart = ensembl) >>> Error in getBM(attributes = c("affy_hg_u133_plus_2", >>> "go_biological_process_id", : >>> Invalid attribute(s): go_biological_process_id >>> Please use the function 'listAttributes' to get valid attribute names >>> >>> I am thus unable to reproduce previous results. >>> Have no idea how this could happen, If anyone can help it will be great. >>> Thanks >>> Konika >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> -- >> >> >> Wolfgang Huber >> EMBL >> http://www.embl.de/research/units/genome_biology/huber >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >
miRNA GO probe limma matchprobes biomaRt arrayQualityMetrics microRNA miRNA GO probe • 1.1k views
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