Steven | 28 Jan 20:41 2013
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Re: BiomaRt: getLDS keeps returning NULL

Hi Steffen,

Thanks for you quick reply, I will try it again next week then.
In reply to you request; I just c/p your lines in above post and it
resulted in said error message.

I don't know if it helps but I did find a remark related to something
similar:

I believe biomaRt package does not
support the new webservice API of biomart v0.8. It should work if your
biomart installation was v0.7.

source:
http://comments.gmane.org/gmane.science.biology.informatics.conductor/40152

I use ubuntu 12.04.1, R2.15

best wishes

Steven

2013/1/28 Steffen Durinck <durinck.steffen@...>

> Hi Steven,
>
> The ensembl web interface has been updated to Ensembl 70 but the BioMart
> interface not yet, this usually happens about a week or so later.  If you
> use listMarts() you can see that biomaRt is still giving  ENSEMBL GENES 69
> (SANGER UK) as version and not 70.  I would expect the BioMart interface to
> be updated soon too and hopefully your query then works.
>
> Can you give the exact query you were attempting to the archive that gave
> you the XML error So I can look into why it fails?
>
> Cheers,
> Steffen
>
>
> On Mon, Jan 28, 2013 at 9:23 AM, Steven <steven.wink@...> wrote:
>
>> Dear list,
>>
>> In relation to above posts, I am also not getting getLDS to work. Steffen
>> mentioned the ensemble 70 release could possibly fix the linking of db's,
>> but it is not working for me yet.
>> using the lines from Nolwenn I also get zero rows output. Using Steffens
>> solution of an archived ensemble version I get an api error:
>>
>> Request to BioMart web service failed. Verify if you are still connected
>> to the internet.  Alternatively the BioMart web service is temporarily
>> down.  Check http://www.biomart.org and verify if this website is
>> available.
>> *Error: XML content does not seem to be XML, nor to identify a file name
>> *
>>
>> I would like to map e.g. affy probe ID's from "affy_hg_u133_plus"_2 to
>> "affy_rat230_2".
>>
>> An alternative solution to using biomaRt would also be super.
>>
>> best Wishes,
>>
>> Steven Wink
>>
>>
>>
>> 2012/11/30 Nolwenn Le Meur <nlemeur@...>
>>
>>> Thank you Steffen for your help. I will do as you suggest.
>>>
>>> Best wishes
>>> Nolwenn
>>>
>>> On Friday, November 30, 2012, Steffen Durinck wrote:
>>>
>>> > Hi Nolwenn,
>>> >
>>> > Ensembl let us know that this is a known bug in the current Ensembl
>>> > release 69 and that it will be fixed in the next release Ensembl 70
>>> which
>>> > is due sometime in january.
>>> > Until that fix, I would suggest you query an archived version of
>>> Ensembl,
>>> > the May release of this year works for example:
>>> >
>>> > library(biomaRt)
>>> > human<-useMart("ENSEMBL_MART_ENSEMBL","hsapiens_gene_ensembl",host="
>>> > may2012.archive.ensembl.org")
>>> > mouse<-useMart("ENSEMBL_MART_ENSEMBL","mmusculus_gene_ensembl",host="
>>> > may2012.archive.ensembl.org")
>>> > getLDS(attributes = c("hgnc_symbol","chromosome_name",
>>> "start_position"),
>>> > filters = "hgnc_symbol", values = "TP53",mart = human,attributesL =
>>> > c("chromosome_name","start_position"), martL = mouse)
>>> >   HGNC.symbol Chromosome.Name Gene.Start..bp. Chromosome.Name.1
>>> > 1        TP53              17         7565097                11
>>> >   Gene.Start..bp..1
>>> > 1          69393861
>>> >
>>> > Cheers,
>>> > Steffen
>>> >
>>> >
>>> >
>>> > On Wed, Nov 28, 2012 at 11:17 AM, Steffen Durinck <
>>> > durinck.steffen@... <javascript:_e({}, 'cvml',
>>>
>>> > 'durinck.steffen@...');>> wrote:
>>> >
>>> >> Hi Nolwenn,
>>> >>
>>> >> It looks like the linking of two datasets is currently broken at the
>>> >> Ensembl side.
>>> >> We've contacted them to look into it and hopefully this can be fixed
>>> soon.
>>> >>
>>> >> Cheers,
>>> >> Steffen
>>> >>
>>> >> On Wed, Nov 28, 2012 at 7:02 AM, Nolwenn Le Meur [guest] <
>>> >> guest@... <javascript:_e({}, 'cvml',
>>>
>>> >> 'guest@...');>> wrote:
>>> >>
>>> >>>
>>> >>> Dear list,
>>> >>>
>>> >>> I am trying to use the getLDS function from the biomaRt package to
>>> get
>>> >>> mouse homolog for human genes but whatever example I take the
>>> function
>>> >>> getLDS keeps returning NULL.
>>> >>>
>>> >>> > human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
>>> >>> > mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl")
>>> >>> > getLDS(attributes = c("hgnc_symbol","chromosome_name",
>>> >>> "start_position"), filters = "hgnc_symbol", values = "TP53",mart =
>>> >>> human,attributesL = c("chromosome_name","start_position"), martL =
>>> mouse)
>>> >>> NULL
>>> >>> Message d'avis :
>>> >>> In getLDS(attributes = c("hgnc_symbol", "chromosome_name",
>>> >>> "start_position"),  :
>>> >>>   getLDS returns NULL.
>>> >>>
>>> >>> Thank you for your help
>>> >>> Nolwenn
>>> >>>
>>> >>>
>>> >>>  -- output of sessionInfo():
>>> >>>
>>> >>> R version 2.15.0 (2012-03-30)
>>> >>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>> >>>
>>> >>> locale:
>>> >>> [1] C
>>> >>>
>>> >>> attached base packages:
>>> >>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>> >>>
>>> >>> other attached packages:
>>> >>> [1] biomaRt_2.12.0       mouse4302.db_2.7.1   BiocInstaller_1.4.9
>>> >>> [4] org.Mm.eg.db_2.7.1   RSQLite_0.11.2       DBI_0.2-5
>>> >>> [7] AnnotationDbi_1.18.4 Biobase_2.16.0       BiocGenerics_0.2.0
>>> >>>
>>> >>> loaded via a namespace (and not attached):
>>> >>> [1] IRanges_1.14.4 RCurl_1.95-3   XML_3.95-0.1   stats4_2.15.0
>>> >>>  tcltk_2.15.0
>>> >>> [6] tools_2.15.0
>>> >>>
>>> >>> --
>>> >>> Sent via the guest posting facility at bioconductor.org.
>>> >>>
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>>> >>
>>> >>
>>> >
>>>
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