[BioC] Biomart mysql error...
lgautier at gmail.com
Tue Dec 2 18:09:44 CET 2008
Jesper Ryge wrote:
> 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
>> 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?
In the meanwhile, you may also consider restricting your query to the
subset of probesets showing differential expression.
>> Jesper Ryge wrote:
>>> 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
>>>> mart <- useMart("ensembl"
>> ,dataset="rnorvegicus_gene_ensembl",mysql=T)> connected to:
>>> Reading database configuration of: rnorvegicus_gene_ensembl
>>> Checking attributes and filters ... ok
>>> Checking main tables ... ok
>>>> test <-
>> 2",values=c("1367452_at","1367453_at"), mart=mart)
>>> Error in mysqlExecStatement(conn, statement, ...) :
>>> RS-DBI driver: (could not run statement: Table
>>> doesn't exist)
>>> the samme session run with mysql=F works fine!
>>> R version 2.8.0 (2008-10-20)
>>> attached base packages:
>>>  stats graphics grDevices utils datasets methods
>>> other attached packages:
>>>  RMySQL_0.6-1 DBI_0.2-4 biomaRt_1.16.0
>>> loaded via a namespace (and not attached):
>>>  RCurl_0.92-0 XML_1.98-1
>>> any help highly appreciated:-)
>>> jesper Ryge
>>> karolinska Institutet
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
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