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

Hi,

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

m1 <- useMart("plants_mart", "osativa_eg_gene", host = "archive.plants.ensembl.org")
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="archive.plants.ensembl.org".

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.

D.

ADD COMMENTlink modified 12 days ago • written 12 days ago by Didi10
0
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 archive.plants.ensembl.org you are actually redirected to mar2016-plants.ensembl.org 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 oct2017-plants.ensembl.org although I can't find any documentation about this, so it may not be permanent. You can query this via:

library(biomaRt)
m1 <- useMart("plants_mart", "osativa_eg_gene", host = "oct2017-plants.ensembl.org")
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Bear in mind with this that all of the information you retrieve from here will be potentially out of date, and it might be worth finding out why the tigr_locus attribute was removed from the current Ensembl release.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
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