Question: biomaRt error message
gravatar for Didi
12 days ago by
Didi10 wrote:


I downloaded the latest version of biomaRt and tried to run:

m1 <- useMart("plants_mart", "osativa_eg_gene", host = "")
go <- getBM(attributes=c("go_accession", "tigr_locus", "entrezgene","go_namespace_1003"),mart=m1)

Since the "tigr_locus" attribute name changed or it's missing in the latest version of biomaRt I used host="".

I got this error.

Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  :
  line 1 did not have 3 elements

Can you tell me how to fix it?

How to get the "tigr_locus" attribute in the latest version? any other name?

Thanks a lot.


ADD COMMENTlink modified 12 days ago • written 12 days ago by Didi10
gravatar for Mike Smith
12 days ago by
Mike Smith3.1k
EMBL Heidelberg / de.NBI
Mike Smith3.1k wrote:

I think this error is because when you go to you are actually redirected to and biomaRt doesn't cope with this redirection.

However if you use the correct URL in your R query you currently encounter a different error. I get this same error when using the Ensembl BioMart web interface, suggesting this is a problem at Ensembl's end, rather than something I can address in biomaRt.

There is a more recent archive at although I can't find any documentation about this, so it may not be permanent. You can query this via:

m1 <- useMart("plants_mart", "osativa_eg_gene", host = "")
go <- getBM(attributes=c("go_id", "tigr_locus", "entrezgene","namespace_1003"), mart=m1)

Bear in mind with this that all of the information you retrieve from here will be potentially out of date, and it might be worth finding out why the tigr_locus attribute was removed from the current Ensembl release. That's something that you will have to contact Ensembl about.

ADD COMMENTlink modified 12 days ago • written 12 days ago by Mike Smith3.1k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 369 users visited in the last hour