User: Mike Smith

gravatar for Mike Smith
Mike Smith890
Reputation:
890
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Trusted
Location:
EMBL Heidelberg / de.NBI
Website:
http://www.msmith.de/
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11 hours ago
Joined:
6 years, 8 months ago
Email:
g********@gmail.com

Posts by Mike Smith

<prev • 53 results • page 1 of 6 • next >
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Comment: C: BioMart: connection fails
... If you're using the same package version then there shouldn't be any difference between which operating system you're using. However the code has change quite a bit across the last ver versions, so I would make sure you are using the latest version (2.38.0) and R 3.5. ...
written 1 day ago by Mike Smith890
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Answer: A: Trying to add ensembl_transcript_id using Biomart
... I think the reason you're getting some NA values is because the gene IDs you are using (taken from `rownames(counts)`) include a version number at the end e.g. "ENSMUSG00000000001.4". Your **biomaRt** query then doesn't match these as your filter specifies the non-versioned IDs to search. Here's a ...
written 8 weeks ago by Mike Smith890
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Answer: A: Biomart package listFilter function with with_mirbase vs other mir information
... The two filters that start `with_` are boolean filters, meaning that take either `TRUE` or `FALSE`. You can use these to return only the entries stored in Ensembl that have a particular type of ID. So if you want the list of all entries that have a mirbase ID you would use the `with_mirbase` filte ...
written 10 weeks ago by Mike Smith890
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Answer: A: biomaRt rnorvegicus_gene_ensembl dataset is not valid!
... There was an issue with **biomaRt** that manifested when Ensembl release 91 introduced datasets with apostrophes in e.g. "Ma's Night Monkey" which would lead to the error you were seeing. See https://support.bioconductor.org/p/104025/#104043 or https://www.biostars.org/p/289654/#289861 If you were ...
written 4 months ago by Mike Smith890
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Comment: C: biomaRt rnorvegicus_gene_ensembl dataset is not valid!
... Can you update your post to include the output of the command `sessionInfo()` so we can see what version of R & biomaRt you are using? ...
written 4 months ago by Mike Smith890
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Answer: A: Find all rsid synonyms for a list of rsids
... You can do this using R and **biomaRt**. Here's an example. First lets create two example sets of SNPS. Between these the first pair are identical, the second pair are synonyms to each other, and the third pair are distinct. snps1 <- c('rs4844600', 'rs4266886', 'rs6656401') snps2 &l ...
written 4 months ago by Mike Smith890
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Comment: C: Obtaining rsIDs using BiomaRt or linux
... You can improve the speed of this approach by noting that you can use a vector of values if you use the `chromosomal_region` filter. This requires that you supply the SNP coordinates in the form *chrom:start:end*. You then don't need a loop or the `do.call` expression, just a single call to `getBM ...
written 4 months ago by Mike Smith890
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Answer: A: How to avoid annotating multiple genes to a single CpG locus?
... I think this is non-trivial. If you look at your PCDHGC example (http://www.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000240184;r=5:141475207-141513719) Ensembl has multiple genes spanning the same region. I don't know the reasoning behind why these are separate genes rather than tran ...
written 5 months ago by Mike Smith890
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Answer: A: BioMart: connection fails
... As Emily has said, parts of Ensembl are down right now. This includes the archive sites and the BioMart interface at the main site. You can check this just by visiting in a browser (http://www.ensembl.org/biomart/martview?redirect=no) - at the moment you get an error page. However you can use one ...
written 6 months ago by Mike Smith890
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Answer: A: Query Genes within regions
... You're correct that a weakness of **biomaRt** is that you can't match the results with a specific part of the query, it just dumps back everything that matched at least once, and querying with each region separately isn't very quick if you have thousands of regions. If you want to do this in R, the ...
written 6 months ago by Mike Smith890

Latest awards to Mike Smith

Teacher 1 day ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Appreciated 6 weeks ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: biomaRt mmusculus_gene_ensembl dataset
Teacher 4 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
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 5 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Appreciated 5 months ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 5 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Appreciated 8 months ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio
Appreciated 8 months ago, created a post with more than 5 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
Teacher 8 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 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
Scholar 9 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 11 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio

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