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 Until that fix, I would suggest you query an archived version of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@gene.com <javascript:_e({}, 'cvml',=""> 'durinck.steffen@gene.com');>> 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@bioconductor.org <javascript:_e({}, 'cvml',="">> 'guest@bioconductor.org');>> 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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>>
>>
>
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