[BioC] biomaRt question

Dipl.-Ing. Johannes Rainer johannes.rainer at tugraz.at
Fri Apr 8 08:39:21 CEST 2005

hi steffen,

i installed the new package, but i have a slightly problem... i can't 
connect to the mart database... i write you the error message that i 

Error in mysqlNewConnection(drv, ...) : RS-DBI driver: (could not 
connect anonymous at ensembldb.ensembl.org on dbname "(null)"

i tried to connect to the database using the dbConnect method and it 
worked, so i think it may be a problem with the dbname = 
databases$ensembl... i have installed the ensembl_mart_30, so the 
database has the same name. i hope the database i installed is the 
right one... i downloaded the whole directory ensembl_mart_30 from 


and installed this according to the howto from


i checked again the martConnect function and am afraid that i do not 
have the right database... if there should be tables in there called 
affy_hg_u133_plus_2 i get a problem, because i do not have those...

can you please help me to find the right database to download? what 
name should this database have?

thanks, jo

Quoting sdurinck at ebi.ac.uk:

> Hi Jo,
> No problem;)
> In attach the biomaRt version with changing host possibilities.
> Would you mind to test if it really works?  I haven't got a local Ensembl
> install so can't really test it but it should work.
> you should now connect using the function:
> mart<-martConnect(host = "your host",user = "username",
> password="yourpasswd")
> Can you let me know if it works or if you run into troubles?
> Cheers,
> Steffen
>> Hi Steffen,
>> thanks for your great support! i will wait for the new package...
>> thanks, jo

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