User: Mike Smith

gravatar for Mike Smith
Mike Smith3.3k
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EMBL Heidelberg / de.NBI
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http://www.msmith.de/
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Posts by Mike Smith

<prev • 523 results • page 1 of 53 • next >
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Comment: C: How to download reference genomes using the RBioMart from ensembl?
... Before we try and work out how to get **biomaRt** working for you, can I ask for some more information on what you're ultimately trying to do in your analysis. If you really want to download entire organism reference genomes, then **biomaRt** probably isn't the tool you want to use. It will take a ...
written 5 days ago by Mike Smith3.3k
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Answer: A: biomaRt retrieving only NAs for Oryza sativa gene descriptions/annotations
... It looks to me like the description is blank if you use the web interface too e.g [Ensembl Plants BioMart][1] If that's the case then you'll need to contact Ensembl to find out why the underlying dataset has changed. It looks like the rice genome was update in the last release, so maybe this is re ...
written 8 days ago by Mike Smith3.3k
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Comment: C: BioMart web service you're accessing may be down
... Does it work any better if you are explicit about using https and the port e.g? ``` listMarts(host = "https://www.ensembl.org", port = 443) ``` ``` biomart version 1 ENSEMBL_MART_ENSEMBL Ensembl Genes 96 2 ENSEMBL_MART_MOUSE Mouse strains 96 3 ENSEMBL_ ...
written 8 days ago by Mike Smith3.3k
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Comment: C: Scanf error in biomaRt when field is missing
... Ensembl won't let you retrieve more than one type of sequence at a time. If you try using the webinterface the different sequence types are selected with a radio button where only one selection is allowed. As far as I'm aware there's no way for the **biomaRt** package to know which attributes are ...
written 9 days ago by Mike Smith3.3k
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Answer: A: Scanf error in biomaRt when field is missing
... Sort term hacky fix, try swapping the order of the attributes you want to return e.g. ``` BM <- biomaRt::getBM(c("ensembl_peptide_id", "ensembl_gene_id", "peptide"), filters = "ensembl_gene_id" , values = "ENSG00000166736", mart = ...
written 9 days ago by Mike Smith3.3k
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Comment: C: Unable to load mzR due to built on Rcpp version (1.0.0)
... Hopefully this suggestion will work. The warning about different Rcpp versions if is pretty common when installing **mzR**, but I think it's being elevated to an error by the **remotes** package, as that's its default behaviour. More details on this and how to change the behaviour can be found at ...
written 12 days ago by Mike Smith3.3k
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Answer: A: Error when retrieving gene name data using biomaRt
... I think Ensembl is currently experiencing some slowdown with their website, leading to a few reports of this in the past couple of days. You can try using a mirror as suggested in https://support.bioconductor.org/p/119983/ However, from your variable names it suggests you're using the Ensembl arch ...
written 12 days ago by Mike Smith3.3k
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Answer: A: Error in biomaRt
... I'm seeing a few reports of this error at the moment, which suggests to me that maybe Ensembl is being quite slow and timing out on your query. Can you try using a different mirror that may be faster? You can do this by running this line before calling `getBM()`: ``` ensembl = useEnsembl( "ensemb ...
written 13 days ago by Mike Smith3.3k
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Comment: C: biomaRt is not working
... I think that was a typo, and should have read 2.34.1, and 2.38.0 should be fine. *Note that the **BiocInstaller** package has been deprecated now, and you should use **BiocManager**. The installation instructions on https://bioconductor.org/packages/biomaRt/ reflect this.* If the problem remains p ...
written 13 days ago by Mike Smith3.3k
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Answer: A: Error in getBM(c("affy_rice", "ensembl_gene_id", "entrezgene", "external_gene_na
... You'll need to load the package where `featureNames()` is defined. This is in **Biobase** rather than **biomaRt**, so you should add the line `library(Biobase)` to the top of your script. If you see an error like this in the future you can search the help files for all the package you have instal ...
written 26 days ago by Mike Smith3.3k

Latest awards to Mike Smith

Teacher 4 months ago, created an answer with at least 3 up-votes. For A: getBM error: The query to the BioMart webservice returned an invalid result
Scholar 4 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 5 months ago, created an answer that has been accepted. For A: How to combine sequences from different stringsets?
Scholar 5 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Is there a way to tell biocLite() to install a Bioconductor package only if it i
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: BioParallel::BatchtoolsParam() - how to pass customized resource variables to ba
Scholar 7 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 8 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 10 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 11 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Is there a way to tell biocLite() to install a Bioconductor package only if it i
Scholar 22 months ago, created an answer that has been accepted. For A: Install problems on centos 7 of TCGAbiolinks
Scholar 22 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Is there a way to tell biocLite() to install a Bioconductor package only if it i
Scholar 22 months ago, created an answer that has been accepted. For A: BiomaRT URLs down? 404 Not Found
Scholar 22 months ago, created an answer that has been accepted. For A: biomaRt error in useMart
Scholar 22 months ago, created an answer that has been accepted. For A: biomaRt: drerio_gene_ensembl dataset missing
Scholar 22 months ago, created an answer that has been accepted. For A: biomaRt is not working
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Please use the function 'listAttributes' to get valid attribute names
Scholar 22 months ago, created an answer that has been accepted. For A: biomaRt scan error for latest assembly when indicating version Number
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: HDF5 reading speed
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Scan error using biomart with version option
Scholar 22 months ago, created an answer that has been accepted. For A: R: error while reading .h5 files from R using rdhf5 package
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: biomaRt: drerio_gene_ensembl dataset missing
Scholar 22 months ago, created an answer that has been accepted. For A: Please use the function 'listAttributes' to get valid attribute names

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