User: Mike Smith

gravatar for Mike Smith
Mike Smith4.0k
Reputation:
3,960
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Location:
EMBL Heidelberg / de.NBI
Website:
http://www.msmith.de/
Last seen:
35 minutes ago
Joined:
9 years, 6 months ago
Email:
g********@gmail.com

Posts by Mike Smith

<prev • 611 results • page 1 of 62 • next >
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Answer: A: Anyone else having trouble with biomaRt (Oct 10, 2019)
... I can reproduce this problem in the Ensembl BioMart web interface. Just select the rat gene dataset and as for any sequence type & it will intermittently return zero results. This indicates it's a problem at Ensembl's end, so I suggest raising a support ticket with them. ...
written 5 days ago by Mike Smith4.0k
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Comment: C: Anyone else having trouble with biomaRt (Oct 10, 2019)
... I just tested rat with the same `useEnsembl()` code you provided, but different mirror arguments. I think it can't be universal because there are normally a ton of questions in short order if Ensembl / biomRt stops working entirely. I'll look more closely tomorrow. ...
written 6 days ago by Mike Smith4.0k
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Comment: C: Anyone else having trouble with biomaRt (Oct 10, 2019)
... I can confirm I'm seeing the same behaviour across several mirrors. This is going to be fun to diagnose! ...
written 6 days ago by Mike Smith4.0k
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Comment: C: Anyone else having trouble with biomaRt (Oct 10, 2019)
... Can you update to include `sessionInfo()` so we can see the biomaRt version you're using. Normally when biomaRt fails to talk to Ensembl correctly you get an error rather than an empty result, so this may be something I haven't seen before. Also, might be worth seeing if the same happens when using ...
written 6 days ago by Mike Smith4.0k
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Comment: C: BioMart does not find mouse homologs of human genes
... Where on the Ensembl page does it show that MIR155HG is conserved between human and mouse? When I look at the orthologues page it suggests that there are none in any of the 27 primate species - perhaps I'm reading that wrong. ...
written 6 days ago by Mike Smith4.0k
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Answer: A: biomaRt getBM failing to retrieve entrezgene
... The `entrezgene` attribute was changed to `entrezgene_id` when Ensembl 97 was released. It was a straightforward renaming, so nothing else should be affected. Thanks for pointing out the broken example in the vignette. I thought I'd caught and updated all instances of this, but that one obviously ...
written 16 days ago by Mike Smith4.0k
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Comment: C: Error when installing Rgraphviz on Centos
... Do you have graphviz installed on your system? (e.g. https://centos.pkgs.org/7/centos-x86\_64/graphviz-devel-2.30.1-21.el7.x86\_64.rpm.html ) It's listed as an 'optional requirement' on the [Rgraphviz][1] homepage, but maybe it's not so optional on CentOS? [1]: http://www.bioconductor.org/packa ...
written 16 days ago by Mike Smith4.0k
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Comment: C: package chorddiag is not available (for R version 3.6.1)
... What command did you run to install the package? It looks like the chorddiag package is only available on Github (https://github.com/mattflor/chorddiag) and there are installation instructions on that page. This also means this isn't really the right place to ask for support with the package, sinc ...
written 22 days ago by Mike Smith4.0k
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Comment: C: Can't install GOSEQ (dependency problem) on CentOS 7!
... I guess it depends if that's feasible. In my case the CentOS machine isn't administered by me, so controlling the system curl version gets challenging. ...
written 26 days ago by Mike Smith4.0k
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Answer: A: Can't install GOSEQ (dependency problem) on CentOS 7!
... I've encountered the same thing and worked around it by installing the previous version of the curl package via: ``` install.packages("https://cran.r-project.org/src/contrib/Archive/curl/curl_4.0.tar.gz", repo=NULL, type="source") ``` Not ideal, but it seems to work and allow the packages that dep ...
written 26 days ago by Mike Smith4.0k

Latest awards to Mike Smith

Scholar 8 weeks ago, created an answer that has been accepted. For A: 'biomaRt expected a character string of length 1' error with getBM and reseq mrn
Scholar 9 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Teacher 9 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
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: 'biomaRt expected a character string of length 1' error with getBM and reseq mrn
Scholar 9 months ago, created an answer that has been accepted. For A: 'biomaRt expected a character string of length 1' error with getBM and reseq mrn
Scholar 9 months ago, created an answer that has been accepted. For A: Error: Bioconductor version '3.8' requires R version '3.5'
Voter 9 months ago, voted more than 100 times.
Scholar 9 months ago, created an answer that has been accepted. For A: How to combine sequences from different stringsets?
Scholar 9 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Error: Bioconductor version '3.8' requires R version '3.5'
Scholar 9 months ago, created an answer that has been accepted. For A: Is there a way to tell biocLite() to install a Bioconductor package only if it i
Scholar 9 months ago, created an answer that has been accepted. For A: Error: Bioconductor version '3.8' requires R version '3.5'
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Error: Bioconductor version '3.8' requires R version '3.5'
Teacher 9 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
Appreciated 9 months ago, created a post with more than 5 votes. For A: Error: Bioconductor version '3.8' requires R version '3.5'
Scholar 10 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Teacher 10 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 11 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: How to combine sequences from different stringsets?
Teacher 12 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 12 months ago, created an answer with at least 3 up-votes. For A: BioParallel::BatchtoolsParam() - how to pass customized resource variables to ba
Scholar 13 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 14 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 16 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 17 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages

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