Scan issue retrieving Drosophila Genes with biomaRt
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JD • 0
@jd-15015
Last seen 6.1 years ago

Hi, 

My guess is I just don't know what I am doing...

The following code worked well prior to December release: 
  mart <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "dmelanogaster_gene_ensembl", host = 'ensembl.org')
  t2g <- getBM(attributes = c("ensembl_transcript_id", "ensembl_gene_id", "external_gene_name", "transcript_biotype"), mart = mart)

But now I have the following error: 
 Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  :  line 1 did not have 3 elements

I have tried 'useEnsembl' and specifying version 90 but that didn't seem to help. mart@host is always "http://e90.ensembl.org:80/biomart/martservice" unless I specify the host as "e91.ensembl.org" in my useMart code above. But I still get the same error regardless.

Is there something simple I am doing wrong? 

R biomart drosophila melanogaster ensembl • 1.5k views
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Entering edit mode
Mike Smith ★ 6.5k
@mike-smith
Last seen 1 day ago
EMBL Heidelberg

This is the same issue seen in biomaRt getBM error in scan

For the host argument you need to explicitly put the 'www ', since there are many possible subdomains for ensembl.org e.g.

mart <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", 
                           dataset = "dmelanogaster_gene_ensembl", 
                           host = "www.ensembl.org")

Both this and the problem you encountered with specifying versions in useEnsembl have been patched in the developmental version of biomaRt.

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