User: Steffen Durinck

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3 years, 9 months ago
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4 years, 4 months ago
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Posts by Steffen Durinck

<prev • 15 results • page 1 of 2 • next >
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Answer: A: biomaRt bug? swapped colnames
... Hi David, That happens with a few query types and the headers are erroneously put on at the BioMart server side, nothing that is fixable from the biomaRt end.  You can overwrite the BioMart headers though with setting bmHeader=FALSE in the getBM query and then things should look fine.  In that case ...
written 3.8 years ago by Steffen Durinck90
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Answer: A: How can I use biomaRt on previus databases?
... Thanks for this answer Jim,  I just wanted to add that getGene function will be phased out very soon to avoid these errors. (It should have been removed a long time ago) Cheers, Steffen   ...
written 3.8 years ago by Steffen Durinck90
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Comment: C: Attributes construct error in biomaRt
... And lastly, The following work around could get you connected: mart = new("Mart",biomart="ensembl",host = "http://www.biomart.org:80/biomart/martservice",archive=FALSE,vschema="default") ensembl = useDataset(mart=mart,dataset="hsapiens_gene_ensembl") I think you should be able to do queries us ...
written 3.9 years ago by Steffen Durinck90
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Comment: C: Attributes construct error in biomaRt
... Could you also check if this solves the issue:   bm = htmlTreeParse("http://www.biomart.org/biomart/martservice?type=registry&requestid=biomaRt")   ...
written 3.9 years ago by Steffen Durinck90
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Comment: C: Attributes construct error in biomaRt
... If the HTML page looks fine in your browser then maybe there is an issue in how your computer parses this data. As I don't have access to Windows, I can't trouble shoot but I think you might be able to do some debugging on the xmlTreeParsing that is used inside biomaRt. See if you can replicate th ...
written 3.9 years ago by Steffen Durinck90
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Answer: A: Attributes construct error in biomaRt
... Hi Sean, What do you get by running: listMarts(verbose=TRUE) or copy paste the URL printed by listMarts in your browser http://www.biomart.org:80/biomart/martservice?type=registry&requestid=biomaRt Maybe that will return a message that give you more info on the problem.  Also check the bio ...
written 3.9 years ago by Steffen Durinck90
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Answer: A: accessing a local 0.8 mart instance with biomaRt
... Hi Christophe. BioMart 0.8 is currently not supported by biomaRt, only BioMart 0.7 is. We are actively working on making biomaRt compatible with BioMart 0.8 and hope to have something ready soon. Best, Steffen ...
written 4.2 years ago by Steffen Durinck90
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Answer: A: cannot connect to REACTOME database in R
... Hi, The Reactome BioMart instance is not being maintained and therefore unfortunately currently not available. Hopefully it will come back online at a future date. Cheers, Steffen   ...
written 4.4 years ago by Steffen Durinck90
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Answer: A: biomaRt: no access to Ensembl_75 (GRCh37.p13)
... Hi Kaoru, I fixed this in the dev version of biomaRt (2.23.1)  now you should be able to use getSequence on biomart ENSEMBL_MART_ENSEMBL Cheers, Steffen   ...
written 4.4 years ago by Steffen Durinck90
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Comment: C: unimart web Service not available
... Hi Kathrin, Unimart will be re-added to the central BioMart service soon, for now you can query the Uniprot BioMart service directly by doing: unimart = useMart("unimart",dataset="uniprot",host="www.ebi.ac.uk ",path="/uniprot/biomart/martservice") Best, Steffen On Tue, May 28, 2013 at 4:20 PM, ...
written 5.8 years ago by Steffen Durinck90

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Scholar 3.8 years ago, created an answer that has been accepted. For A: Attributes construct error in biomaRt

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