[BioC] too many biomaRt connections

[Kasper Daniel Hansen]

Steffen will know more about this, but it is well known that when you  
access the Mart servers that you should collect all your queries into  
one big query, so not do something like
   for ( g in genes)
     getInfo(g)
but instead do something like
   getInfo(genes)

So try to collect everything into a few big queries, instead of doing  
"thousands of queries" in a day.

You also have the option of downloading the entire database and access  
it locally. That way there is no limit, but it requires some work

It is not uncommon for these large databases to have some usage limits.

Kasper

On Apr 9, 2008, at 12:09 PM, Elizabeth Purdom wrote:

> Hi,
> I am using biomaRt to get information regarding genes. I use it pretty
> frequently and recently have gotten the error:
>
> Too many connections at
> /ebi/www/biomart/www/biomart-perl-06/lib/BioMart/Configuration/ 
> DBLocation.pm
> line 98
>
> I assume that I've hit some sort of wall in terms of how often I have
> queried the database?
>
> I don't really use biomart except through R; at what point do you get
> booted off and what can I do to regain access? I often run queries  
> on a
> few hundred genes and don't think twice about rerunning such a query  
> or
> running several such queries in a day plus I use functions that call  
> on
> biomaRt repeatedly that I also apply to around 100 genes. So I could
> easily send a thousand queries in a day. I can be more careful, but it
> would be useful to know what the limits are. And does it matter how  
> many
> times you call a 'mart<-useMart(...)' command? (lately, I've been
> calling it frequently rather than using the one I've already opened,
> largely through programming laziness).
>
> By the way, it took me quite some time to track down the error,  
> because
> I was using getGene which just gave me the confusing error:
> "Error: ncol(result) == length(attributes) is not TRUE"
> I think this must be because something like try(...) is used within
> getBM() and so the output is the error message which is then  
> transferred
> down the line and at some point causes a problem when the function  
> tries
> to bundle it into a data.frame, etc.
>
> Thanks,
> Elizabeth
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor