Question: Error in biomart connection
1
gravatar for shivangi.agarwal800
5 months ago by
shivangi.agarwal80070 wrote:

Hi

When using following code in R, I am getting error

lolliplot(mutation_data, fillCol="mutation_type", labelCol="amino_acid_change", proteinColour = "#ffffff", paletteB ="green", txtSize=3, txtAngle=20, host="dec2013.archive.ensembl.org")

Using the following host: dec2013.archive.ensembl.org for biomaRt queries to change the ensembl annotation version alter this parameter!
Querying biomaRt for transcript sequence
Request to BioMart web service failed.
The BioMart web service you're accessing may be down.
Check the following URL and see if this website is available:
http://dec2013.archive.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
Error in if (!grepl(x = registry, pattern = "^\n*<MartRegistry>")) { : 
  argument is of length zero

How to solve this?

ensembl biomart R • 266 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by shivangi.agarwal80070

Origin of error is clear Request to BioMart web service failed.. Does that suggested link work for you?

ADD REPLYlink modified 5 months ago • written 5 months ago by zx87547.9k

Thanks so much Smith. The given links are working.

ADD REPLYlink written 5 months ago by shivangi.agarwal80070
4
gravatar for Mike Smith
5 months ago by
Mike Smith1.3k
EMBL Heidelberg / de.NBI
Mike Smith1.3k wrote:

That particular Ensembl archive is no longer available. You can view the list of available archives by following the link in the error message (you'll be redirected to an appropriate page) or by using the listEnsemblArchives() function in biomaRt e.g.

> biomaRt::listEnsemblArchives()
             name     date                                url version current_release
1  Ensembl GRCh37 Feb 2014          http://grch37.ensembl.org  GRCh37                
2      Ensembl 95 Jan 2019 http://jan2019.archive.ensembl.org      95               *
3      Ensembl 94 Oct 2018 http://oct2018.archive.ensembl.org      94                
4      Ensembl 93 Jul 2018 http://jul2018.archive.ensembl.org      93                
5      Ensembl 92 Apr 2018 http://apr2018.archive.ensembl.org      92                
6      Ensembl 91 Dec 2017 http://dec2017.archive.ensembl.org      91                
7      Ensembl 90 Aug 2017 http://aug2017.archive.ensembl.org      90                
8      Ensembl 89 May 2017 http://may2017.archive.ensembl.org      89                
9      Ensembl 88 Mar 2017 http://mar2017.archive.ensembl.org      88                
10     Ensembl 87 Dec 2016 http://dec2016.archive.ensembl.org      87                
11     Ensembl 86 Oct 2016 http://oct2016.archive.ensembl.org      86                
12     Ensembl 85 Jul 2016 http://jul2016.archive.ensembl.org      85                
13     Ensembl 84 Mar 2016 http://mar2016.archive.ensembl.org      84                
14     Ensembl 83 Dec 2015 http://dec2015.archive.ensembl.org      83                
15     Ensembl 82 Sep 2015 http://sep2015.archive.ensembl.org      82                
16     Ensembl 81 Jul 2015 http://jul2015.archive.ensembl.org      81                
17     Ensembl 80 May 2015 http://may2015.archive.ensembl.org      80                
18     Ensembl 79 Mar 2015 http://mar2015.archive.ensembl.org      79                
19     Ensembl 78 Dec 2014 http://dec2014.archive.ensembl.org      78                
20     Ensembl 77 Oct 2014 http://oct2014.archive.ensembl.org      77                
21     Ensembl 76 Aug 2014 http://aug2014.archive.ensembl.org      76                
22     Ensembl 75 Feb 2014 http://feb2014.archive.ensembl.org      75                
23     Ensembl 67 May 2012 http://may2012.archive.ensembl.org      67                
24     Ensembl 54 May 2009 http://may2009.archive.ensembl.org      54
ADD COMMENTlink written 5 months ago by Mike Smith1.3k
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