Question: Biomart Error in using listMarts()
0
gravatar for vivekphilip
12 weeks ago by
vivekphilip0 wrote:

I get the following error message when I try to access biomart via R. code : listMarts() error : Error in listMarts(host = host, path = path, port = port, includeHosts = TRUE, : Unexpected format to the list of available marts.

However, I can navigate to this page http://useast.ensembl.org/biomart/martservice?type=registry&requestid=biomaRt

Please let me know what needs to be done to fix this

Regards, Vivek

job url error • 104 views
ADD COMMENTlink written 12 weeks ago by vivekphilip0
1

Can you update your post to include the output of sessionInfo() so we can see what versions of R and biomaRt you are using.

If you're running listMarts() with no other options then you shouldn't be ending up on the useast mirror site, so some redirection is taking place somewhere. Since the mirror is working for you in the browser, you can try specifying it explicitly in your call e.g.

listMarts(host = "http://useast.ensembl.org")

As an aside, when using this forum, it's helpful to add the name of the package you're trying to use as a 'tag' so the package author gets notified by email of any activity. I'd also advise removing 'job' as this just makes the post look like spam to me!

ADD REPLYlink written 12 weeks ago by Mike Smith3.8k
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