User: Mike Smith

gravatar for Mike Smith
Mike Smith250
Reputation:
250
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Trusted
Location:
EMBL Heidelberg / de.NBI
Website:
http://www.msmith.de/
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1 day, 3 hours ago
Joined:
5 years, 6 months ago
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g********@gmail.com

Posts by Mike Smith

<prev • 22 results • page 1 of 3 • next >
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Answer: A: Retrieving phytozome data using the R bioconductor package biomaRt
... Short answer is that I think for now you have to bypass some of the **biomaRt** functions, and create a `Mart` object yourself. So give this a try: library(biomaRt) phytozomeMart <- new("Mart", biomart = "phytozome_mart", vschema = "zome_mart" ...
written 14 days ago by Mike Smith250
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Comment: C: Converting between Ensembl Versions
... Version 2.33.4 of **biomaRt** now contains the function `listEnsemblArchives()` which will display all the available archives and the URL used to access them: > listEnsemblArchives() version date url [1,] "Ensembl GRCh37" "Feb 20 ...
written 7 weeks ago by Mike Smith250
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Answer: A: Converting between Ensembl Versions
... To answer your other question about the Ensembl archives with **biomaRt**, I think the `archive = TRUE` arguments are now long out of date. You can access mirrors using the appropriate URL to `host` and just ignoring the `archive` argument entirely e.g. for Ensembl 87 > listMarts(host = "ht ...
written 7 weeks ago by Mike Smith250
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Answer: A: Retrieve all genes under a mammalian phenotype ontology term
... I'm not sure you can do this using Ensembl's BioMart. There you can filter using specific phenotype ontology terms, but only leaf terms rather than something quite high level like MP:0005375 which is Adipose Tissue Phenotype and has many sub-terms. I don't think you can query using the phenotype I ...
written 4 months ago by Mike Smith250
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Comment: C: vector dimension limit in biomaRt
... If you want to use the devel version of **biomaRt** and report back here whether it's fixed the problem or not that would be perfect. Since it takes a few days for changes to propagate through the Bioc build system, I find the easiest way to install a devel package is with: source("https://bio ...
written 4 months ago by Mike Smith250
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Answer: A: vector dimension limit in biomaRt
... I've modified the `getBM()` function in **biomaRt** to submit queries in batches if the number of values exceeds 500. If you have multiple filters each of which have more than 500 values it should generate multiple mutually exclusive queries so that all combinations are run without breaking the 500 ...
written 4 months ago by Mike Smith250
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Comment: C: vector dimension limit in biomaRt
... Thanks, that'd be great. You can send it to grimbough [at] gmail [dot] com. Cheers. ...
written 4 months ago by Mike Smith250
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Comment: C: vector dimension limit in biomaRt
... Yes, it almost feels deterministic sometimes, but I don't know exactly what drives it. Presumably the search takes the same amount of time every time you run it, and then it times out at the same point. There was a bit more discussion on the Bioconductor support site a while ago at [https://suppor ...
written 4 months ago by Mike Smith250
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Answer: A: vector dimension limit in biomaRt
... This is probably because the BioMart back end tends to cope badly (but silently) with queries containing more than about 500 entries. Admittedly I don't think this is documented anywhere in **biomaRt**, so that's not easy to figure out. If you use the web interface it warns you next to the filter. ...
written 4 months ago by Mike Smith250
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Answer: A: Xenopus tropicalis Ensembl Gene IDs and Transcripts ID with BiomaRt
... If you want to get all values for the attributes you're interested in, you don't need to supply any **filters** or **values**. The following query should return all available data, but bear in mind it might take a long time to run. library(biomaRt) ensembl <- useMart('ensembl', ...
written 4 months ago by Mike Smith250

Latest awards to Mike Smith

Teacher 14 days ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 14 days ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
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
Scholar 4 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Autobiographer 5 months ago, has more than 80 characters in the information field of the user's profile.
Appreciated 3.6 years ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio

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