[BioC] biomaRt error: useMart fails

[michael watson (IAH-C)]

Hi Steffen

I have solved the problem by specifically installing RMySQL:

>biocLite(RMySQL) 

And then using the "mysql=T" option to useMart.

I now have another problem.  I want to retrieve ensembl stable ids for
genes, along with chromosomal location.  The documentation says I can do
this, however, it does not work as advertised.

> ychrom <- getFeature(chromosome = "Y", mart = mart, type="entrezgene")
> ychrom
An object of class "martTable"
Slot "id":
  [1] "6736"   "6192"   "7544"   etc
Slot "table":
$chromosome
  [1] "Y" "Y" "Y" "Y etc
$start
  [1]  2714896  2769527  2863322  etc
$end
  [1]  2715740  2794997  2910547  etc

I took this code from the biomaRt.pdf document, and in there the above
code returns ensembl stable ids.

At the end, I want a list of ensembl gene or transcript stable ids,
along with start and end chromosomal location: is this possible?

Many thanks

Mick

-----Original Message-----
From: Steffen Durinck [mailto:durincks at mail.nih.gov] 
Sent: 06 July 2006 15:17
To: michael watson (IAH-C)
Cc: Bioconductor
Subject: Re: [BioC] biomaRt error: useMart fails

Hi Mick,

This should only happen when you do not have an internet connection or 
the Ensembl website goes down.  Make sure you are online and try again.

best,
Steffen

michael watson (IAH-C) wrote:
> Hi
>
> Sorry if this has been covered before, I did search the archives but I
> didn't find a solution.
>
> I'm using R 2.3.1 on windows and bioMart 1.6.0 (the BioC 1.8 release
> version)
>
>   
>> library(biomaRt)
>>     
> Loading required package: XML
> Loading required package: RCurl
> Warning message:
> use of NULL environment is deprecated 
>
>   
>> mart <- useMart("ensembl")
>>     
> Error in curlPerform(curl = curl, .opts = opts) : 
>         couldn't connect to host
>
>   
>> mart <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
>>     
> Error in curlPerform(curl = curl, .opts = opts) : 
>         couldn't connect to host
>
> I know some people have been getting this "couldn't connect to host"
> error before, but I didn't find a solution.
>
> Many thanks
>
> Mick
>
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