On Wed, Nov 18, 2009 at 5:13 PM, <mauede@alice.it> wrote:

> I would get  huge amount of data to parse.
> Is there any example of batch query ?
>
>
Hi, Maura.  You may want to read the biomart vignette if you haven't done
so.  There are a number of examples in there.  If you are having problems or
questions, please post the code (a reproducible example), and error messages
along with the output of sessionInfo().

Sean

-----Messaggio originale-----
> Da: tc.fhcrc@gmail.com per conto di Tony Chiang
> Inviato: mer 18/11/2009 18.30
> A: mauede@alice.it
> Cc: Steffen@stat.berkeley.edu; Bioconductor List; Stefano Rovetta
> Oggetto: Re: [BioC] BioMart error occurred again
>
> I think that you have asked this question (a number of times) before.
> Please
> see Steffen's answer to you via the link (and please note Sean's requests):
>
>
> http://thread.gmane.org/gmane.science.biology.informatics.conductor/25759/focus=25778
>
> Within a 7 hour period, there could be a number of things that can occur
> between your connection to Biomart. Batch queries would be the way forward
> as per Steffen's comments if you are not already doing this.
>
>
> On Wed, Nov 18, 2009 at 8:38 AM, <mauede@alice.it> wrote:
>
> > This time the following error occurred after roughly 7-hour no-stop
> > running.
> >
> >
> >
> >  OPEN NEW CONNECTION ON FILE:   hsa-miR-199a-5p_V_MirBase_FastaFiles.txt
> >
> >  **** WRITE 3UTR SEQUENCE TO FILE:
> > hsa-miR-199a-5p_V_MirBase_FastaFiles.txt  ****
> > Error in getBM(attributes = c("hgnc_symbol", "ensembl_gene_id",
> > "refseq_dna",  :
> >  Query ERROR: caught BioMart::Exception::Database: Could not connect to
> > mysql database ensembl_mart_56: DBI
> connect('database=ensembl_mart_56;host=
> > martdb.ensembl.org;port=5316','anonymous',...) failed: Can't connect to
> > MySQL server on 'martdb.ensembl.org' (110) at /srv/biomart_server/
> > biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98
> > > sessioninfo()
> > Error: could not find function "sessioninfo"
> > > infosession()
> > Error: could not find function "infosession"
> > > sessionInfo()
> > R version 2.9.0 (2009-04-17)
> > x86_64-unknown-linux-gnu
> >
> > locale:
> >
> >
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] tools     stats     graphics  grDevices utils     datasets  methods
> > [8] base
> >
> > other attached packages:
> >  [1] JGR_1.6-7         iplots_1.1-3      JavaGD_0.5-2      rJava_0.6-3
> >  [5] CORNA_1.2         XML_2.5-1         GEOquery_2.8.0    RCurl_0.98-1
> >  [9] bitops_1.0-4.1    biomaRt_2.0.0     Biobase_2.4.1     gdata_2.4.2
> > [13] microRNA_1.2.0    Rlibstree_0.3-2   Biostrings_2.12.7 IRanges_1.2.3
> >
> > loaded via a namespace (and not attached):
> > [1] gtools_2.6.1
> >
> >
> > tutti i telefonini TIM!
> >
> >
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> >
> > _______________________________________________
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> > Search the archives:
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> >
>
>
>
>
> tutti i telefonini TIM!
>
>
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>
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