User: Mike Smith

gravatar for Mike Smith
Mike Smith1.4k
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1,360
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Location:
EMBL Heidelberg / de.NBI
Website:
http://www.msmith.de/
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4 hours ago
Joined:
7 years, 8 months ago
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g********@gmail.com

Posts by Mike Smith

<prev • 77 results • page 1 of 8 • next >
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Comment: C: From ensembl id to protein structure
... A nice answer, but I just wanted to point out that **biomaRt** will be really slow if you do this in a loop for a large number of Ensembl IDs. It will work much better if you pass the vector of IDs to the `values` argument e.g. ensembl <- useEnsembl('ensembl', dataset = 'hsapiens_gene_ensem ...
written 9 weeks ago by Mike Smith1.4k
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Answer: A: Mapping Entrez gene ids to Ensembl ids
... The fundamental issue here is that your `entrezgene` object is a `tibble` with one column, where as the `getBM()` function expects to be passed a vector. The internal code doesn't handle this very well and throws the error you saw. When you run `tbl <- mapply(tbl, FUN=as.numeric)` you get bac ...
written 9 weeks ago by Mike Smith1.4k
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Comment: C: biomaRt: Cannot access the zebra fish dataset
... I would recommend you start a new topic with this question since it is unlikely to be the same issue as reported here, and include some details of the code you have already tried. ...
written 9 weeks ago by Mike Smith1.4k
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Comment: C: Get gene symbols from gene ids for mouse using BioMart
... Perhaps you want to try the `entrezgene_id` filter instead? getBM(attributes = c("ensembl_gene_id", "external_gene_name"), filters = "entrezgene_id", values = entrzID, mart = ensembl) ensembl_gene_id external_gene_name 1 ENSMUSG00000040415 ...
written 3 months ago by Mike Smith1.4k
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Answer: A: What is the gold standard for the one-to-many relationships in BioMart retrieved
... The reason you get multiple results to your biomaRt query is that Ensembl BioMart is transcript-centric. If you also asked for the `ensembl_transcript_id` attribute you'd see this was different for each row. As far as filtering goes, this surely depends upon that data you already have i.e. are you ...
written 3 months ago by Mike Smith1.4k
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Answer: A: Unable to access ensembl biomart archives via R
... Are you still experiencing this error? I get the same correct response as Genomax when I test your example code. If it's now working for you then I suspect it was a temporary outage of the Ensembl site, and biomaRt didn't handle it very gracefully. If not the please post the output of `sessionInf ...
written 3 months ago by Mike Smith1.4k
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Comment: C: annotation - biomaRt - getBM - multiple entrez ID
... Try using the attribute `entrezgene_id` instead. Ensembl changed this in release 97, which only just came out (http://ftp.ensembl.org/pub/release-97/release_97_biomart_changes.txt ). ...
written 4 months ago by Mike Smith1.4k
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Answer: A: R: How to save Mart object (BiomaRt package)
... I think there's a few issues here, but the fundamental problem in your example is that `ensembl` is an object of class **Mart** not a table of results. It stores various information about the 'Mart' (which you can think of a resource) such as the URL and properties of dataset you want to access suc ...
written 4 months ago by Mike Smith1.4k
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Comment: C: vector dimension limit in biomaRt
... No need to bump this old post. You're getting lots of responses from the Ensembl team at https://www.biostars.org/p/384170/ and I responded to your cross posted query at https://support.bioconductor.org/p/121827/ ...
written 5 months ago by Mike Smith1.4k
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Comment: C: converting mouse emsembl gene IDs to Gene names by bioMart and gconvert with n
... Just want to add that you can use the `searchFilters()` function to find the appropriate filters in one step e.g. > searchFilters(m_ensembl, "exon") name description 55 ensembl_exon_id Exon ID(s) [e.g. ENSMUSE00000097910] ...
written 5 months ago by Mike Smith1.4k

Latest awards to Mike Smith

Supporter 5 weeks ago, voted at least 25 times.
Good Answer 8 weeks ago, created an answer that was upvoted at least 5 times. For A: biomaRt mmusculus_gene_ensembl dataset
Appreciated 8 weeks ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 3 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 7 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 8 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Scholar 8 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 9 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Guru 10 months ago, received more than 100 upvotes.
Appreciated 11 months ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: biomaRt mmusculus_gene_ensembl dataset
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: biomaRt mmusculus_gene_ensembl dataset
Appreciated 13 months ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 16 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term

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