[BioC] Biomart mysql error...

[Laurent Gautier]

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 
>> 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?



In the meanwhile, you may also consider restricting your query to the 
subset of probesets showing differential expression.





L.




> 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
>>>
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