biomaRt fails to connect
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rmporsch • 0
@rmporsch-9349
Last seen 9.0 years ago

I used the guidlines of the BiomaRt (3.2) package to connect to ensembl by using

```

useMart("ensembl",dataset="hsapiens_gene_ensembl")

```

 

 

but I get the following error:

```

Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Opening and ending tag mismatch: hr line 7 and body
Opening and ending tag mismatch: body line 4 and html
Premature end of data in tag html line 2
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Opening and ending tag mismatch: hr line 7 and body
5: Opening and ending tag mismatch: body line 4 and html
6: Premature end of data in tag html line 2

```

 

also

 

```

ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)

```

 

returns the same error.

biomaRt • 1.5k views
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Entering edit mode
Thomas Maurel ▴ 800
@thomas-maurel-5295
Last seen 22 months ago
United Kingdom

Hello,

The syntax that you used above is only working with the new function called "useEnsembl" from BiomaRt 3.2. You can either do:

* With useMart (biomaRt <= 3.2)

ensembl <- useMart(biomart="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", path="/biomart/martservice", dataset="hsapiens_gene_ensembl")

* With useEnsembl (biomaRt == 3.2)

ensembl <- useEnsembl(biomart="ensembl",dataset="hsapiens_gene_ensembl")

 

The useDataset function should then work with either call.

Hope this helps,

Regards,

Thomas

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