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Question: Scan issue retrieving Drosophila Genes with biomaRt
0
gravatar for JD
10 weeks ago by
JD0
JD0 wrote:

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? 

ADD COMMENTlink modified 10 weeks ago by Mike Smith2.6k • written 10 weeks ago by JD0
0
gravatar for Mike Smith
10 weeks ago by
Mike Smith2.6k
EMBL Heidelberg / de.NBI
Mike Smith2.6k wrote:

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.

ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by Mike Smith2.6k
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