[BioC] Biomart mysql error...

[steffen at stat.Berkeley.EDU]

Hi Jesper,

biomaRt gets information about tables from an xml description inside the
database.  It looks like for some reason the table that biomaRt associates
with the rat chip is incorrect.  I'll investigate and fix it if the
problem is at the biomaRt side.

Your query shouldn't be slow when you set mysql=F.  The BioMart
webservices are pretty fast.  Setting mysql=F is the preferred way to use
biomaRt as it is better supported by the BioMart developers and relies
less on the query building we do on the R side with mysql=T (which is
harder to maintain when things change in new Ensembl releases).

Cheers,
Steffen




> thanx laurent :-)
>
>
> ----- Original Message -----
> From: Laurent Gautier <lgautier at gmail.com>
> Date: Monday, December 1, 2008 7:16 pm
> Subject: Re: [BioC] Biomart mysql error...
> To: Jesper.Ryge at ki.se
> Cc: "bioconductor mail list bioconductor at stat.math.ethz.ch"
> <bioconductor at stat.math.ethz.ch>
>
>>
>> The issue is likely on the server end (updates of the database
>> structure).
>> I think that sql=TRUE will "only" provide a faster data retrieval.
>>
>> You can keep=FALSE in the meanwhile.
>
> hm, could be. but the problem persisted since friday and its still
> there... i wanted to update
> annotation from the whole affy_rat230 chip so its a rather big query and i
> assume mysql
> handle this better... ill brace myself with patience, but should it take
> so long to correct if its
> an error in their end (ensembl database update or something)? does anybody
> know if this is
> the case and when it will be up and running again?
>
> cheers,
> jesper
>
>>
>>
>> Jesper Ryge wrote:
>> > Hi
>> >
>> > im running into a biomaRt problem when i use the mysql=T in
>> useMart which has worked
>> > very well earlier on my computer (MacPro3,1 )???  Here is a short
>> illustration:
>> >
>> >> library(biomaRt)
>> >
>> >>  mart <- useMart("ensembl"
>> ,dataset="rnorvegicus_gene_ensembl",mysql=T)> connected to:
>> ensembl
>> > Reading database configuration of: rnorvegicus_gene_ensembl
>> > Checking attributes and filters ... ok
>> > Checking main tables ... ok
>> >
>> >> test <-
>> >
>>
> getBM(attributes=c("ensembl_gene_id","external_gene_id","description"),filters="affy_rat230_
>> 2",values=c("1367452_at","1367453_at"), mart=mart)
>> > Error in mysqlExecStatement(conn, statement, ...) :
>> >   RS-DBI driver: (could not run statement: Table
>> 'ensembl_mart_51.ox_AFFY_Rat230_2__dm'
>> > doesn't exist)
>> >
>> > the samme session run with mysql=F works fine!
>> >
>> >> sessionInfo()
>> > R version 2.8.0 (2008-10-20)
>> > i386-apple-darwin9.5.0
>> >
>> > locale:
>> > C/UTF-8/C/C/C/C
>> >
>> > attached base packages:
>> > [1] stats     graphics  grDevices utils     datasets  methods
>> base
>> >
>> > other attached packages:
>> > [1] RMySQL_0.6-1   DBI_0.2-4      biomaRt_1.16.0
>> >
>> > loaded via a namespace (and not attached):
>> > [1] RCurl_0.92-0 XML_1.98-1
>> >
>> > any help highly appreciated:-)
>> >
>> > cheers,
>> > jesper Ryge
>> > karolinska Institutet
>> >
>> > _______________________________________________
>> > 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
>>
>