Hi
I am having some trouble in using the biomart package.
I get this error message :
/Error in mysqlExecStatement(conn, statement, ...) : RS-DBI driver:
(could not run statement: Table
'ensembl_mart_38.hsapiens_gene_ensembl__structure__dm' doesn't exist)/
when executing this command
*getBM(attributes=listAttributes(martMm)[202],
filters=listFilters(martMm)[15], values=listT , mart=martMm)
with
**listAttributes(martMm)[202]=**"mmusculus_gene_ensembl_structure.exon
_stable_id_v"
and **listFilters(martMm)[15] = *
where martMm has been created this way :* martMm <- useMart(biomart =
"ensembl", dataset="mmusculus_gene_ensembl",
host="ensembldb.ensembl.org", mysql=TRUE)
*Can someone help me please
thank you.
*
*
--
MOUROT Tabar?
Stagiaire Master Pro BioInfo
Plateforme transcriptome
Institut de G?nomique Fonctionnelle
141, rue de la Cardonille
34094 Montpellier Cedex 5
Tel : +33 (0)4 67 14 29 64
E-mail : tabare.mourot at igf.cnrs.fr
--
Passerelle antivirus IGF
--
Dear Tabare,
we recommend to use the biomaRt package in the webservice mode. The
direct access to the Ensembl database tables via MySQL relies one some
hard coded assumptions which may not apply to the particular table you
are looking at, also there has recently been a new Ensembl release,
which might complicate things.
For this reason please use the webservice access to biomarts, which is
not prone to these problems.
Best wishes
-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax: +44 1223 494486
Http: www.ebi.ac.uk/huber
-------------------------------------
TM wrote:
> Hi
> I am having some trouble in using the biomart package.
> I get this error message :
> /Error in mysqlExecStatement(conn, statement, ...) : RS-DBI
driver:
> (could not run statement: Table
> 'ensembl_mart_38.hsapiens_gene_ensembl__structure__dm' doesn't
exist)/
> when executing this command
> *getBM(attributes=listAttributes(martMm)[202],
> filters=listFilters(martMm)[15], values=listT , mart=martMm)
> with
> **listAttributes(martMm)[202]=**"mmusculus_gene_ensembl_structure.ex
on_stable_id_v"
> and **listFilters(martMm)[15] = *
> where martMm has been created this way :* martMm <- useMart(biomart
=
> "ensembl", dataset="mmusculus_gene_ensembl",
> host="ensembldb.ensembl.org", mysql=TRUE)
>
> *Can someone help me please
> thank you.
>
Thank you for your help. I am now using the 1.5.17 biomaRt package to
use the webservice mode but using the webservice mode i still have
problems with the getHomolog fonction :
/> getHomolog(id="NM_000015", from.type="refseq", to.type="refseq",
from.mart=martHs, to.mart=martMm)
V1
1 ERROR::Attribute gene_stable_id NOT FOUND
2 ERROR::Attribute transcript_stable_id NOT FOUND
/and also with the "hsapiens_gene_ensembl_structure.exon_stable_id_v"
attribute I get an error whereas it works with others attributes :
/(getBM(attributes="hsapiens_gene_ensembl_structure.exon_stable_id_v",
filters="refseq_dna", values="NM_000015", mart=martHs))/
/
2
<html><head>
3 <title>500 Internal Server
Error</title>
4
</head><body>
5
Internal
Server
Error
6 The server encountered an
internal error or
7 misconfiguration and was
unable
to complete
8
your
request.
9 Please contact the server
administrator,
10 webmaster@mydomain.org and inform them of the time the
error occurred,
11 and anything you might have done
that may have
12 caused
the error.
13 More information about this error may
be available
14 in the server
error log.
15
</body></html>/
Is it coming from the ensembl databases ?
regards,
Tabar? Mourot
Wolfgang Huber a ?crit :
> Dear Tabare,
>
> we recommend to use the biomaRt package in the webservice mode. The
> direct access to the Ensembl database tables via MySQL relies one
some
> hard coded assumptions which may not apply to the particular table
you
> are looking at, also there has recently been a new Ensembl release,
> which might complicate things.
>
> For this reason please use the webservice access to biomarts, which
is
> not prone to these problems.
>
> Best wishes
> -------------------------------------
> Wolfgang Huber
> European Bioinformatics Institute
> European Molecular Biology Laboratory
> Cambridge CB10 1SD
> England
> Phone: +44 1223 494642
> Fax: +44 1223 494486
> Http: www.ebi.ac.uk/huber
> -------------------------------------
>
>
> TM wrote:
>> Hi
>> I am having some trouble in using the biomart package.
>> I get this error message :
>> /Error in mysqlExecStatement(conn, statement, ...) : RS-DBI
>> driver: (could not run statement: Table
>> 'ensembl_mart_38.hsapiens_gene_ensembl__structure__dm' doesn't
exist)/
>> when executing this command
>> *getBM(attributes=listAttributes(martMm)[202],
>> filters=listFilters(martMm)[15], values=listT , mart=martMm)
>> with
>> **listAttributes(martMm)[202]=**"mmusculus_gene_ensembl_structure.e
xon_stable_id_v"
>>
>> and **listFilters(martMm)[15] = *
>> where martMm has been created this way :* martMm <- useMart(biomart
=
>> "ensembl", dataset="mmusculus_gene_ensembl",
>> host="ensembldb.ensembl.org", mysql=TRUE)
>>
>> *Can someone help me please
>> thank you.
>>
>
--
MOUROT Tabar?
Stagiaire Master Pro BioInfo
Plateforme transcriptome
Institut de G?nomique Fonctionnelle
141, rue de la Cardonille
34094 Montpellier Cedex 5
Tel : +33 (0)4 67 14 29 64
E-mail : tabare.mourot at igf.cnrs.fr
--
Passerelle antivirus IGF
--
Dear Tabare,
biomaRt tries to contain as minimal as possible hard coded information
on
the BioMart databases and as such to be robust to new BioMart database
releases. The getBM function contains no hard-coded information on
the
databases and should always work. The 'simpler' biomaRt functions
such as
getGene and getHomolog do contain hard-coded information on the
attributes
to query and as such are prone to database changes.
The new release of Ensembl (which this time contained quite some
changes)
co-incided with a new release of Bioconductor. I've had to change the
biomaRt code so it could work with the old and new Ensembl version.
The biomaRt version (1.6.0) that is included in Bioconductor release
1.8
can deal with both Ensembl releases and your getHomolog query works:
> martHs = useMart("ensembl",dataset="hsapiens_gene_ensembl")
Checking attributes and filters ... ok
> martMm = useMart("ensembl",dataset="mmusculus_gene_ensembl")
Checking attributes and filters ... ok
> getHomolog(id="NM_000015", from.type="refseq", to.type="refseq",
+ from.mart=martHs, to.mart=martMm)
V1 V2 V3
1 ENSMUSG00000051147 ENSMUST00000070766
2 ENSMUSG00000051147 ENSMUST00000093470 NM_010874
The second error you give is a bug.
The attribute "hsapiens_gene_ensembl_structure.exon_stable_id_v"
should
not be present in the output of listAttributes as it involves multiple
BioMart datasets to be combined to make the query. Currently only the
getHomolog function can combine two datasets (i.e. two species).
Best,
Steffen
> Thank you for your help. I am now using the 1.5.17 biomaRt package
to
> use the webservice mode but using the webservice mode i still have
> problems with the getHomolog fonction :
> /> getHomolog(id="NM_000015", from.type="refseq", to.type="refseq",
> from.mart=martHs, to.mart=martMm)
> V1
> 1 ERROR::Attribute gene_stable_id NOT FOUND
> 2 ERROR::Attribute transcript_stable_id NOT FOUND
>
> /and also with the
"hsapiens_gene_ensembl_structure.exon_stable_id_v"
> attribute I get an error whereas it works with others attributes :
>
/(getBM(attributes="hsapiens_gene_ensembl_structure.exon_stable_id_v",
> filters="refseq_dna", values="NM_000015", mart=martHs))/
> /
> 2
> <html><head>
> 3 <title>500 Internal
Server
> Error</title>
> 4
> </head><body>
> 5
Internal
Server
> Error
> 6 The server encountered an
> internal error or
> 7 misconfiguration and was
unable
> to complete
> 8
your
> request.
> 9 Please contact the server
> administrator,
> 10 webmaster@mydomain.org and inform them of the time the
> error occurred,
> 11 and anything you might have
done
> that may have
> 12
caused
> the error.
> 13 More information about this error
may
> be available
> 14 in the
server
> error log.
> 15
> </body></html>/
>
> Is it coming from the ensembl databases ?
> regards,
>
> Tabar? Mourot
>
> Wolfgang Huber a ?crit :
>> Dear Tabare,
>>
>> we recommend to use the biomaRt package in the webservice mode. The
>> direct access to the Ensembl database tables via MySQL relies one
some
>> hard coded assumptions which may not apply to the particular table
you
>> are looking at, also there has recently been a new Ensembl release,
>> which might complicate things.
>>
>> For this reason please use the webservice access to biomarts, which
is
>> not prone to these problems.
>>
>> Best wishes
>> -------------------------------------
>> Wolfgang Huber
>> European Bioinformatics Institute
>> European Molecular Biology Laboratory
>> Cambridge CB10 1SD
>> England
>> Phone: +44 1223 494642
>> Fax: +44 1223 494486
>> Http: www.ebi.ac.uk/huber
>> -------------------------------------
>>
>>
>> TM wrote:
>>> Hi
>>> I am having some trouble in using the biomart package.
>>> I get this error message :
>>> /Error in mysqlExecStatement(conn, statement, ...) : RS-DBI
>>> driver: (could not run statement: Table
>>> 'ensembl_mart_38.hsapiens_gene_ensembl__structure__dm' doesn't
exist)/
>>> when executing this command
>>> *getBM(attributes=listAttributes(martMm)[202],
>>> filters=listFilters(martMm)[15], values=listT , mart=martMm)
>>> with
>>> **listAttributes(martMm)[202]=**"mmusculus_gene_ensembl_structure.
exon_stable_id_v"
>>>
>>> and **listFilters(martMm)[15] = *
>>> where martMm has been created this way :* martMm <-
useMart(biomart =
>>> "ensembl", dataset="mmusculus_gene_ensembl",
>>> host="ensembldb.ensembl.org", mysql=TRUE)
>>>
>>> *Can someone help me please
>>> thank you.
>>>
>>
>
> --
> MOUROT Tabar?
> Stagiaire Master Pro BioInfo
> Plateforme transcriptome
> Institut de G?nomique Fonctionnelle
> 141, rue de la Cardonille
> 34094 Montpellier Cedex 5
>
> Tel : +33 (0)4 67 14 29 64
> E-mail : tabare.mourot at igf.cnrs.fr
>
>
> --
> Passerelle antivirus IGF
> --
>
> _______________________________________________
> 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
>
>
Internal Server Error
6 The server encountered an internal error or 7 misconfiguration and was unable to complete 8 your request.9 Please contact the server administrator, 10 webmaster@mydomain.org and inform them of the time the error occurred, 11 and anything you might have done that may have 12 caused the error.
13 More information about this error may be available 14 in the server error log.
15 </body></html>/ Is it coming from the ensembl databases ? regards, Tabar? Mourot Wolfgang Huber a ?crit : > Dear Tabare, > > we recommend to use the biomaRt package in the webservice mode. The > direct access to the Ensembl database tables via MySQL relies one some > hard coded assumptions which may not apply to the particular table you > are looking at, also there has recently been a new Ensembl release, > which might complicate things. > > For this reason please use the webservice access to biomarts, which is > not prone to these problems. > > Best wishes > ------------------------------------- > Wolfgang Huber > European Bioinformatics Institute > European Molecular Biology Laboratory > Cambridge CB10 1SD > England > Phone: +44 1223 494642 > Fax: +44 1223 494486 > Http: www.ebi.ac.uk/huber > ------------------------------------- > > > TM wrote: >> Hi >> I am having some trouble in using the biomart package. >> I get this error message : >> /Error in mysqlExecStatement(conn, statement, ...) : RS-DBI >> driver: (could not run statement: Table >> 'ensembl_mart_38.hsapiens_gene_ensembl__structure__dm' doesn't exist)/ >> when executing this command >> *getBM(attributes=listAttributes(martMm)[202], >> filters=listFilters(martMm)[15], values=listT , mart=martMm) >> with >> **listAttributes(martMm)[202]=**"mmusculus_gene_ensembl_structure.e xon_stable_id_v" >> >> and **listFilters(martMm)[15] = * >> where martMm has been created this way :* martMm <- useMart(biomart = >> "ensembl", dataset="mmusculus_gene_ensembl", >> host="ensembldb.ensembl.org", mysql=TRUE) >> >> *Can someone help me please >> thank you. >> > -- MOUROT Tabar? Stagiaire Master Pro BioInfo Plateforme transcriptome Institut de G?nomique Fonctionnelle 141, rue de la Cardonille 34094 Montpellier Cedex 5 Tel : +33 (0)4 67 14 29 64 E-mail : tabare.mourot at igf.cnrs.fr -- Passerelle antivirus IGF --
Internal Server > Error
> 6 The server encountered an > internal error or > 7 misconfiguration and was unable > to complete > 8 your > request.> 9 Please contact the server > administrator, > 10 webmaster@mydomain.org and inform them of the time the > error occurred, > 11 and anything you might have done > that may have > 12 caused > the error.
> 13 More information about this error may > be available > 14 in the server > error log.
> 15 > </body></html>/ > > Is it coming from the ensembl databases ? > regards, > > Tabar? Mourot > > Wolfgang Huber a ?crit : >> Dear Tabare, >> >> we recommend to use the biomaRt package in the webservice mode. The >> direct access to the Ensembl database tables via MySQL relies one some >> hard coded assumptions which may not apply to the particular table you >> are looking at, also there has recently been a new Ensembl release, >> which might complicate things. >> >> For this reason please use the webservice access to biomarts, which is >> not prone to these problems. >> >> Best wishes >> ------------------------------------- >> Wolfgang Huber >> European Bioinformatics Institute >> European Molecular Biology Laboratory >> Cambridge CB10 1SD >> England >> Phone: +44 1223 494642 >> Fax: +44 1223 494486 >> Http: www.ebi.ac.uk/huber >> ------------------------------------- >> >> >> TM wrote: >>> Hi >>> I am having some trouble in using the biomart package. >>> I get this error message : >>> /Error in mysqlExecStatement(conn, statement, ...) : RS-DBI >>> driver: (could not run statement: Table >>> 'ensembl_mart_38.hsapiens_gene_ensembl__structure__dm' doesn't exist)/ >>> when executing this command >>> *getBM(attributes=listAttributes(martMm)[202], >>> filters=listFilters(martMm)[15], values=listT , mart=martMm) >>> with >>> **listAttributes(martMm)[202]=**"mmusculus_gene_ensembl_structure. exon_stable_id_v" >>> >>> and **listFilters(martMm)[15] = * >>> where martMm has been created this way :* martMm <- useMart(biomart = >>> "ensembl", dataset="mmusculus_gene_ensembl", >>> host="ensembldb.ensembl.org", mysql=TRUE) >>> >>> *Can someone help me please >>> thank you. >>> >> > > -- > MOUROT Tabar? > Stagiaire Master Pro BioInfo > Plateforme transcriptome > Institut de G?nomique Fonctionnelle > 141, rue de la Cardonille > 34094 Montpellier Cedex 5 > > Tel : +33 (0)4 67 14 29 64 > E-mail : tabare.mourot at igf.cnrs.fr > > > -- > Passerelle antivirus IGF > -- > > _______________________________________________ > 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 > >