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Question: biomaRt package problem
0
gravatar for StevenVanLaere
2.0 years ago by
Belgium
StevenVanLaere0 wrote:

All,

anyone recently encountered problems with the biomaRt package?

Steven

 

 

ADD COMMENTlink modified 2.0 years ago by Thomas Maurel700 • written 2.0 years ago by StevenVanLaere0
1
gravatar for Johannes Rainer
2.0 years ago by
Johannes Rainer1.1k
Italy
Johannes Rainer1.1k wrote:

without knowing what problem you have it's hard to answer... but eventually you might find a solution to your problem on that post:

biomaRt no longer works with proxy after upgrade

cheers, jo

ADD COMMENTlink written 2.0 years ago by Johannes Rainer1.1k
1
gravatar for Thomas Maurel
2.0 years ago by
Thomas Maurel700
United Kingdom
Thomas Maurel700 wrote:

Dear Steven,

I am afraid this is because listMarts is looking at the biomart.org website by default which is temporarily down at the moment.

The function accepts an host argument so if you are interested in the Ensembl marts, you can run the following:

> listMarts(host="www.ensembl.org")
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 82
2     ENSEMBL_MART_SNP  Ensembl Variation 82
3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 82
4    ENSEMBL_MART_VEGA               Vega 62
5                pride        PRIDE (EBI UK)

or 

> listEnsembl()
     biomart               version
1    ensembl      Ensembl Genes 82
2        snp  Ensembl Variation 82
3 regulation Ensembl Regulation 82
4       vega               Vega 62
5      pride        PRIDE (EBI UK)

Then you can connect to the Ensembl marts by running:

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

or 

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

You can find more information on the following blog post: http://www.ensembl.info/blog/2015/06/01/biomart-or-how-to-access-the-ensembl-data-from-r/

Hope this helps,

Thomas

ADD COMMENTlink modified 2.0 years ago by Wolfgang Huber13k • written 2.0 years ago by Thomas Maurel700
0
gravatar for StevenVanLaere
2.0 years ago by
Belgium
StevenVanLaere0 wrote:

The problem is that the error messages I get are different depending on time point AND computer.... This is what I get now:

> library(biomaRt)

>listMarts()

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

> sessionInfo()

R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.1 (El Capitan)

locale:
[1] nl_BE.UTF-8/nl_BE.UTF-8/nl_BE.UTF-8/C/nl_BE.UTF-8/nl_BE.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.26.0

loaded via a namespace (and not attached):
 [1] IRanges_2.4.1        parallel_3.2.2       DBI_0.3.1            tools_3.2.2         
 [5] RCurl_1.95-4.7       Biobase_2.30.0       AnnotationDbi_1.32.0 RSQLite_1.0.0       
 [9] S4Vectors_0.8.1      BiocGenerics_0.16.1  stats4_3.2.2         bitops_1.0-6        
[13] XML_3.98-1.3  

Last week I got a message that the BioMart web service was temporarily down...

 

 

 

ADD COMMENTlink written 2.0 years ago by StevenVanLaere0

Any news on this yet? I'm getting the same problem :/

ADD REPLYlink written 2.0 years ago by Mark Dunning1.0k

Dear Mark,

Please see my answer above: A: biomaRt package problem

Hope this helps,

Regards,

Thomas

ADD REPLYlink written 2.0 years ago by Thomas Maurel700

biomaRt has been updated to 2.26.1 in release and 2.27.1 in devel (except for Mac OS 'snow leopard'), to point to ensembl by default. So after updating (via biocLite("biomaRt")) the function listMarts() will work; there may be additional problems with existing scripts or other packages that assume that the connection still points to biomart.org.

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by Martin Morgan ♦♦ 20k

Ooops. Sorry didn't see that. Thanks

Mark

ADD REPLYlink written 24 months ago by Mark Dunning1.0k

Thanks!

 

ADD REPLYlink written 24 months ago by StevenVanLaere0

Thanks!

 

ADD REPLYlink written 24 months ago by StevenVanLaere0
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