User: Mike Smith

gravatar for Mike Smith
Mike Smith4.0k
Reputation:
4,040
Status:
Trusted
Location:
EMBL Heidelberg / de.NBI
Website:
http://www.msmith.de/
Last seen:
7 hours ago
Joined:
9 years, 8 months ago
Email:
g********@gmail.com

Posts by Mike Smith

<prev • 628 results • page 1 of 63 • next >
0
votes
0
answers
60
views
0
answers
Comment: C: Error while opening Mart with biomaRt package
... The certainly sounds like it could be behind the issue, and might explain why you see a difference between the browser and R session. I don't know what will have caused the difference, but I don't think I have made any changes in biomaRt that would have introduce a change like this. Local IT are p ...
written 15 hours ago by Mike Smith4.0k
0
votes
0
answers
60
views
0
answers
Comment: C: Error while opening Mart with biomaRt package
... When I run those commands I get the following: ``` httr::GET("https://www.ensembl.org:443/biomart/martservice?type=registry&requestid=biomaRt") Response [https://www.ensembl.org:443/biomart/martservice?type=registry&requestid=biomaRt] Date: 2019-12-13 10:50 Status: 200 Content-Type: t ...
written 19 hours ago by Mike Smith4.0k
0
votes
0
answers
60
views
0
answers
Comment: C: Error while opening Mart with biomaRt package
... The standard server at www.ensembl.org is hosted in Cambridge, UK and so would typically be the best to use in Europe. I would suggest updating your R to version 3.6 as the version you're using is now a couple of years old, and versions of Bioconductor packages are tied to R versions, so you end up ...
written 1 day ago by Mike Smith4.0k
0
votes
0
answers
60
views
0
answers
Comment: C: Error while opening Mart with biomaRt package
... Something odd is happening, because that's exactly what you should see. The "Unexpected format to the list of available marts" error is only thrown if it doesn't find a page that starts with ``. Since you do see that page, something different must be occurring when using R vs your browser. Could ...
written 1 day ago by Mike Smith4.0k
0
votes
1
answer
38
views
1
answers
Comment: C: Convert Chromosome postions to hgnc_symbol using R
... The currently used reference sequence versions for all vertebrates can be found on this page: https://www.ensembl.org/info/about/species.html By default, when you don't provide a `host` to the `useEnsembl()` function, it will use `www.ensembl.org` and that will then use the most recent refence gen ...
written 1 day ago by Mike Smith4.0k
0
votes
0
answers
60
views
0
answers
Comment: C: Error while opening Mart with biomaRt package
... What do you see if you click on the link in the error message and open it in a web browser? ...
written 2 days ago by Mike Smith4.0k
1
vote
1
answer
38
views
1
answers
Answer: A: Convert Chromosome postions to hgnc_symbol using R
... This seems to work for me if I run the following code based on your examples: ``` ## Create example data.frame with genomic positions positions <- data.frame(chromosome = c(1,1), start = c(62920, 16863509), end = c(16855942, 16932568)) ## load pac ...
written 2 days ago by Mike Smith4.0k
0
votes
0
answers
60
views
0
answers
Comment: C: Error while opening Mart with biomaRt package
... Can you provide a small reproducible example of the code you're running? ...
written 2 days ago by Mike Smith4.0k
0
votes
2
answers
74
views
2
answers
Answer: A: PureCN version clashes at GitHub and Bioconductor
... When I look at the Bioc devel webpage for PureCN (http://bioconductor.org/packages/devel/bioc/html/PureCN.html) I see version 1.17.1. The `RELEASE_3_5`, `Release_3_6` etc branches correspond to Bioconductor releases rather than PureCN specifically. The most recent release is `RELEASE_3_10`. These ...
written 18 days ago by Mike Smith4.0k
1
vote
1
answer
58
views
1
answers
Comment: C: biomaRt expected a character string of length 1
... This is certainly how `values` is intended to be provided, but I think biomaRt will simply unlist the `values` in this case and it should still work. More likely switching to using the the US mirror avoids a timeout with the main site. I would recommend following James' example and defining the ...
written 21 days ago by Mike Smith4.0k

Latest awards to Mike Smith

Scholar 4 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 11 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Teacher 11 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 11 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 11 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 11 months ago, created an answer that has been accepted. For A: Error: Bioconductor version '3.8' requires R version '3.5'
Voter 11 months ago, voted more than 100 times.
Scholar 11 months ago, created an answer that has been accepted. For A: How to combine sequences from different stringsets?
Scholar 11 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Error: Bioconductor version '3.8' requires R version '3.5'
Scholar 11 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 11 months ago, created an answer that has been accepted. For A: Error: Bioconductor version '3.8' requires R version '3.5'
Good Answer 11 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 11 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 11 months ago, created a post with more than 5 votes. For A: Error: Bioconductor version '3.8' requires R version '3.5'
Scholar 12 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Teacher 12 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 13 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 13 months ago, created an answer that has been accepted. For A: How to combine sequences from different stringsets?
Teacher 14 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 14 months ago, created an answer with at least 3 up-votes. For A: BioParallel::BatchtoolsParam() - how to pass customized resource variables to ba
Scholar 15 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 18 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 19 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 147 users visited in the last hour