[BioC] biomaRt question

[Dipl.-Ing. Johannes Rainer]

thanks, it works!

i had to change the hgu133plus2 into hg_u133_plus_2 and it worked then.
thanks for all your help :)
cheers, jo

Quoting Steffen Durinck <sdurinck at ebi.ac.uk>:

> I forgot to mention that in this version we started using the ensembl 
> names for species so now to use homo sapiens you should use hsapiens 
> instead of homo_sapiens.  A list of valid species names can be 
> obtained using the function getSpecies.  Also we use the ensembl 
> names of the affy arrays.
> hgu95av2 now becomes hg_u95av2.  Again a list of valid names can be 
> obtained using the function getAffyArrays.
>
> best,
> Steffen
>
> Dipl.-Ing. Johannes Rainer wrote:
>
>> Hi Steffen,
>>
>> i checked the database, the database should be ok (i have installed 
>> the whole ensembl_mart_30, but without the vega_mart and the 
>> snp_mart, because i didn't find them...). my ensembl_mart_30 has the 
>> hsapiens... affy... table. but when i try to connect to the database 
>> (which is not really installed locally at my notebook, but on our 
>> server) i get alwys the same exception
>>
>> Error in mysqlNewConnection(drv, ...) : RS-DBI driver: (could not 
>> connect anonymous at ensembldb.ensembl.org on dbname "(null)"
>> )
>>
>> have you tried to connect to your local database with the network 
>> cable unplugged, so that you also have no connection to the ensembl 
>> db?
>> the biomaRt package i have installed has the version 1.02, is this 
>> the right one?
>>
>> thanks for your help!
>> cheers, jo
>>
>>
>> Quoting sdurinck at ebi.ac.uk:
>>
>>> Hi Jo,
>>>
>>> I got things working here...
>>> As I don't have enough space on my laptop I did a minimal install using
>>> only two tables as a test.
>>>
>>> in mysql:
>>>
>>> create database ensembl_mart_30
>>>
>>> then in your command line:
>>>
>>> mysql -D ensembl_mart_30 -u DBMAN -p < ensembl_mart_30.sql
>>>
>>> mysqlimport -L -u DBMAN -p  ensembl_mart_30
>>> hsapiens_gene_ensembl__gene__main.txt.table
>>>
>>> mysqlimport -L -u DBMAN -pDBMAN  ensembl_mart_30
>>> sapiens_gene_ensembl__xref_affy_hg_u133_plus_2__dm.txt.table
>>>
>>> mysqlimport -L -u DBMAN -pDBMAN  ensembl_mart_30 
>>> meta_release_info.txt.table
>>>
>>> now I have a mini ensembl install with the human gene info and mapping of
>>> the affy hgu133plus2 id's to ensembl.  To work you also need the
>>> meta_release_info table.
>>>
>>> in R I could do now:
>>>
>>> mart<-martConnect(host="localhost",user="DBMAN", password="DBMAN")
>>> getGene(id="201131_s_at",array="hgu133plus2",mart=mart)
>>>
>>> and the getGene function retrieved the correct result.
>>>
>>> Did you installed ensembl the same way?  it's important that your database
>>> has the name ensembl_mart_30 (or with any other version number) otherwise
>>> it won't work.
>>>
>>> Cheers,
>>> Steffen
>>>
>>> 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 got:
>>>
>>> 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 ensembl:
>>>
>>> ftp://ftp.ensembl.org/pub/current_mart/data/mysql/
>>>
>>> and installed this according to the howto from
>>>
>>> http://www.ebi.ac.uk/biomart/DB_install.html
>>>
>>> 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
>>>
>>
>>
>>
>>
>
>