biomaRt error message: Error in textConnection(bmResult) : invalid 'text' argument
0
1
Entering edit mode
bd2000 ▴ 30
@5d657c1d
Last seen 12 weeks ago
United Kingdom

Hi everyone, I'm having issues with my code below:

 ensembl <- useEnsembl(biomart = "ensembl",
                        host = "www.ensembl.org",
                        dataset = "hsapiens_gene_ensembl"
                        )

This is the error message I keep getting:

Error in textConnection(bmResult) : invalid 'text' argument

I've looked through a couple of other queries on this website and I've tried to change the host/mirror but unfortunately nothing has worked for me. I've checked and it works when I use "grch37.ensembl.org" as a host, however, I do need GRCh38 and not 37. Has anyone else experienced this and know how to fix it?

biomaRt • 619 views
ADD COMMENT
0
Entering edit mode

Is this still the case today? Running you code example works for me.

I think it might have been a transient issue. Unfortunately, the Ensembl BioMart server is notoriously slow and can be unreliable at busy times.

ADD REPLY
1
Entering edit mode

It seems to be working today! Thank you for your help, I wasn't sure if it was just an issue with me or with biomaRt in general

ADD REPLY

Login before adding your answer.

Traffic: 592 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6