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Question: biomaRt fails to connect
0
gravatar for rmporsch
2.9 years ago by
rmporsch0
rmporsch0 wrote:

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.

ADD COMMENTlink modified 2.9 years ago by Thomas Maurel750 • written 2.9 years ago by rmporsch0
0
gravatar for Thomas Maurel
2.9 years ago by
Thomas Maurel750
United Kingdom
Thomas Maurel750 wrote:

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

ADD COMMENTlink written 2.9 years ago by Thomas Maurel750
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