User: Mike Smith

gravatar for Mike Smith
Mike Smith1.6k
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Location:
EMBL Heidelberg / de.NBI
Website:
http://www.msmith.de/
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2 days, 7 hours ago
Joined:
8 years, 7 months ago
Email:
g********@gmail.com

Posts by Mike Smith

<prev • 90 results • page 1 of 9 • next >
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Comment: C: getBM error while using bioMart
... This code works for me at the moment,but it looks like some of the other archive sites are down (you get a 'down for maintenance' page in a browser) and will produces this same error. Hopefully this is only a temporary thing, but I think it is a server-side Ensembl issue rather than something I can ...
written 14 days ago by Mike Smith1.6k
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Comment: C: getBM error while using bioMart
... Currently, if I go to https://sep2019.archive.ensembl.org/ I get the message: > Server Status > The Ensembl web service you requested is temporarily unavailable. We are working to restore the service as soon as possible, and apologise for any inconvenience caused. This is a larger Ensembl is ...
written 14 days ago by Mike Smith1.6k
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Comment: C: getBM error while using bioMart
... This should now be fixed in biomaRt version 2.45.9. ...
written 15 days ago by Mike Smith1.6k
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Comment: C: getBM error while using bioMart
... This seems a weird one. If you run the function `listEnsemblArchives()` do you also get the error? That is the function that tries to read that URL, and in version 2.45.8 it should not be trying to read the `http` version. ...
written 16 days ago by Mike Smith1.6k
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Comment: C: getBM error while using bioMart
... Can you provide an example of the code that leads to the error? ...
written 16 days ago by Mike Smith1.6k
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Comment: C: is there a soln to Error in scan file = file, what = what, sep = sep, quote = qu
... You've posted in two threads with different reports, but not included the code you're running or exactly which error you're encountering. Is it: Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 1 did not have 3 elements" or Error: failed to loa ...
written 17 days ago by Mike Smith1.6k
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Answer: A: is there a soln to Error in scan file = file, what = what, sep = sep, quote = qu
... With the latest version of R and biomaRt I'm unable to reproduce this at the moment (see the example code below). The error almost certainly doesn't related to you input file, but rather to whatever is being returned by the Ensembl BioMart server. This is normally a text file, which biomaRt reads ...
written 18 days ago by Mike Smith1.6k
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Comment: C: getBM error while using bioMart
... I would suggest starting a new R session. Then you can run: ## This install the latest version of biomaRt BiocManager::install('grimbough/biomaRt') ## This loads the newly installed package library(biomaRt) ## Check the version of the package - the latest is 2.45.5 packag ...
written 21 days ago by Mike Smith1.6k
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Answer: A: getBM error while using bioMart
... My initial assement is that something has changed on the Ensembl website, which now doesn't allow access via `http`. If you go to http://www.ensembl.org in your browser it will automatically redirect you to use `https`; the code in biomaRt is failing rather than following the re-direct. Can you tr ...
written 21 days ago by Mike Smith1.6k
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Answer: A: Loop to retrieve rsID out of chrID list
... It looks like you got a working solution, but I just wanted to add that you don't need to do this in a loop at all. You can use the `chromosomal_region` filter and then give a vector of values where each element is the form `chrom:start:end`. This should be much quicker than looping over each loca ...
written 3 months ago by Mike Smith1.6k

Latest awards to Mike Smith

Appreciated 18 days ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 21 days ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Commentator 21 days ago, created a comment with at least 3 up-votes. For C: annotation - biomaRt - getBM - multiple entrez ID
Appreciated 3 months ago, created a post with more than 5 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 3 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 4 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
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: annotation - biomaRt - getBM - multiple entrez ID
Supporter 12 months ago, voted at least 25 times.
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 13 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 14 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 18 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Scholar 19 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 20 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 20 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Guru 22 months ago, received more than 100 upvotes.

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