User: Mike Smith

gravatar for Mike Smith
Mike Smith1.5k
Reputation:
1,500
Status:
Trusted
Location:
EMBL Heidelberg / de.NBI
Website:
http://www.msmith.de/
Last seen:
1 month ago
Joined:
8 years, 4 months ago
Email:
g********@gmail.com

Posts by Mike Smith

<prev • 81 results • page 1 of 9 • next >
2
votes
1
answer
164
views
1
answers
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 5 weeks ago by Mike Smith1.5k
3
votes
2
answers
126
views
2
answers
Answer: A: lift over gene ids rat to human
... Cool that you got another solution. The issue in your original biomaRt approach is that the **MGI Symbol** is specifically for the mouse genome, in the same way that **HGNC Symbol** relates to the human genome. For rat you need to use the **RGD Symbol**. Otherwise, your code looks great e.g. ...
written 5 weeks ago by Mike Smith1.5k
5
votes
1
answer
182
views
1
answers
Answer: A: biomart webservice error when using data from Phytozome
... The solution here is to make sure you include `https://` in the host argument for Phytozome. If that isn't included the query is redirected back to the main Phytozome page rather than the BioMart service, R receives the home page HTML rather than a results table, and thus it fails. library(bio ...
written 7 weeks ago by Mike Smith1.5k
2
votes
1
answer
182
views
1
answers
Comment: C: biomart webservice error when using data from Phytozome
... The two error messages are caused by the same issue, but the wording was changed somewhere between version 2.40 and 2.44. A generic "Error in `scan().. `" is less helpful to diagnose an issue than a message saying the problem is the number of columns in the result table, but really they're the sa ...
written 8 weeks ago by Mike Smith1.5k
1
vote
1
answer
329
views
1
answers
Comment: C: From ensembl id to protein structure
... A nice answer, but I just wanted to point out that **biomaRt** will be really slow if you do this in a loop for a large number of Ensembl IDs. It will work much better if you pass the vector of IDs to the `values` argument e.g. ensembl <- useEnsembl('ensembl', dataset = 'hsapiens_gene_ensem ...
written 10 months ago by Mike Smith1.5k
6
votes
1
answer
344
views
1
answers
Answer: A: Mapping Entrez gene ids to Ensembl ids
... The fundamental issue here is that your `entrezgene` object is a `tibble` with one column, where as the `getBM()` function expects to be passed a vector. The internal code doesn't handle this very well and throws the error you saw. When you run `tbl <- mapply(tbl, FUN=as.numeric)` you get bac ...
written 11 months ago by Mike Smith1.5k
0
votes
2
answers
1.2k
views
2
answers
Comment: C: biomaRt: Cannot access the zebra fish dataset
... I would recommend you start a new topic with this question since it is unlikely to be the same issue as reported here, and include some details of the code you have already tried. ...
written 11 months ago by Mike Smith1.5k
1
vote
1
answer
7.6k
views
1
answers
Comment: C: Get gene symbols from gene ids for mouse using BioMart
... Perhaps you want to try the `entrezgene_id` filter instead? getBM(attributes = c("ensembl_gene_id", "external_gene_name"), filters = "entrezgene_id", values = entrzID, mart = ensembl) ensembl_gene_id external_gene_name 1 ENSMUSG00000040415 ...
written 11 months ago by Mike Smith1.5k
1
vote
1
answer
321
views
1
answers
Answer: A: What is the gold standard for the one-to-many relationships in BioMart retrieved
... The reason you get multiple results to your biomaRt query is that Ensembl BioMart is transcript-centric. If you also asked for the `ensembl_transcript_id` attribute you'd see this was different for each row. As far as filtering goes, this surely depends upon that data you already have i.e. are you ...
written 12 months ago by Mike Smith1.5k
0
votes
1
answer
503
views
1
answers
Answer: A: Unable to access ensembl biomart archives via R
... Are you still experiencing this error? I get the same correct response as Genomax when I test your example code. If it's now working for you then I suspect it was a temporary outage of the Ensembl site, and biomaRt didn't handle it very gracefully. If not the please post the output of `sessionInf ...
written 12 months ago by Mike Smith1.5k

Latest awards to Mike Smith

Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 5 weeks ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Scholar 7 weeks ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: annotation - biomaRt - getBM - multiple entrez ID
Supporter 10 months ago, voted at least 25 times.
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: biomaRt mmusculus_gene_ensembl dataset
Appreciated 10 months ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 12 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 16 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 17 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Scholar 17 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 18 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
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Guru 19 months ago, received more than 100 upvotes.
Appreciated 20 months ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Good Answer 20 months ago, created an answer that was upvoted at least 5 times. For A: biomaRt mmusculus_gene_ensembl dataset
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1166 users visited in the last hour