data acquisition using biomaRt

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maedakus ▴ 10

@maedakus-9484

Last seen 8.3 years ago

Hi, all .

i am very new to bioconductor, and now i am planning to analyze data from BioMart web.

when using R package "biomaRt", i was not able to access biomart web,

and the error message came out as below.

would you mind teaching me how to solve this ?

thanks in advance.

Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.
 error  XML content does not seem to be XML

biomart • 1.9k views

ADD COMMENT • link 8.8 years ago maedakus ▴ 10

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Maybe your firewall settings? Can you access:

http://www.biomart.org

ADD REPLY • link 8.8 years ago b.nota ▴ 370

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Hello,

I am afraid the BioMart portal is down for the moment as they are in the process of migrating hosting.

You can still use BiomaRt by connecting directly to the various mart providers listed on the following page: http://www.biomart.org/notice.html and using the "host" argument of the "useMart" function. E.g for the Ensembl gene mart:

useMart(biomart="ENSEMBL_MART_ENSEMBL",host="www.ensembl.org",dataset="hsapiens_gene_ensembl")