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@gmail.com> 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@gmail.com>
>
>> 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 Until that fix, I would suggest you query an archived version of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.
>> >>>
>> >>> _______________________________________________
>> >>> Bioconductor mailing list
>> >>> Bioconductor@r-project.org <javascript:_e({}, 'cvml',
>> >>> 'Bioconductor@r-project.org');>
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>> >>> Search the archives:
>> >>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>> >>>
>> >>
>> >>
>> >
>>
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