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chawla
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@chawla-4416
Last seen 10.2 years ago
Hi
I had also tried
ensembl=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
goterms=getBM(attributes = c("affy_hg_u133a_2",
"go_biological_process_id","entrezgene"), filters = "affy_hg_u133a_2",
values = data[,1], mart = ensembl)
but got the same error
I guess its because of change in Go attribute names.
Thanks
Konika
On 18-05-2011 12:00, bioconductor-request at r-project.org wrote:
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> 1. Re: Go terms attributes not available on Biomart ensembl
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----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 17 May 2011 08:52:28 -0400
> From: Steve Lianoglou<mailinglist.honeypot at="" gmail.com="">
> To: Wolfgang Huber<whuber at="" embl.de="">
> Cc: bioconductor at r-project.org
> Subject: Re: [BioC] Go terms attributes not available on Biomart
> ensembl
> Message-ID:<banlkti=3zfd5hawds=yxpqngxsh97++6=a at="" mail.gmail.com="">
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi,
>
> There was an email to this list a few days ago about a similar (I
> think) problem with GO queries failing. It seems appropriate
here(?).
> Apparently the identifiers for GO stuffs has changed, see the thread
> that starts here:
>
> https://stat.ethz.ch/pipermail/bioconductor/2011-May/039435.html
>
> The original poster was querying with something like:
>
> attributes=c("entrezgene",
> "go_cellular_component_id",
> "go_cellular_component__dm_name_1006")
>
> And was getting errors.
>
> Apparently:
>
> """the three GO sections have been merged into one. See here for
news about
> ensembl BioMart changes:
>
> http://www.ensembl.org/info/website/news/index.html#team-Mart
>
> These are the names of the attributes you now need to look for:
>
>
>
> <query virtualschemaname="default" formatter="TSV" header="0"> uniqueRows = "0" count = "" datasetConfigVersion = "0.6">
>
> <dataset name="hsapiens_gene_ensembl" interface="default">
> <attribute name="go_id"/>
> <attribute name="name_1006"/>
> <attribute name="definition_1006"/>
> <attribute name="go_linkage_type"/>
> <attribute name="namespace_1003"/>
> </dataset>
> </query>
>
> These attribute names correspond to:
>
> GO Term Accession
> GO Term Name
> GO Term Definition
> GO Term Evidence Code
> GO domain
> """"
>
> Hope that helps,
>
> -steve
>
>
>
> On Tue, May 17, 2011 at 2:44 AM, Wolfgang Huber<whuber at="" embl.de="">
wrote:
>> Konika
>>
>> thanks. Your 'sample code' is incomplete. How did you define the
object
>> 'ensembl'?
>>
>> ? ? ? ?Best wishes
>> ? ? ? ?Wolfgang
>>
>>
>> chawla scripsit 05/15/2011 11:53 PM:
>>> Hi
>>> I have used BiomaRt to retrieve GO terms for affymetrix probe Ids
using
>>> mart ensembl.
>>> But suddenly all the GO terms attributes have vanished from the
list of
>>> attributes.
>>> I used the sample code to test.
>>>
>>> ?> affyids = c("202763_at", "209310_s_at", "207500_at")
>>> ?> getBM(attributes = c("affy_hg_u133_plus_2",
>>> "go_biological_process_id", "chromosome_name", "start_position",
>>> + "end_position", "band"), filters = "affy_hg_u133_plus_2", values
=
>>> affyids, mart = ensembl)
>>> Error in getBM(attributes = c("affy_hg_u133_plus_2",
>>> "go_biological_process_id", :
>>> Invalid attribute(s): go_biological_process_id
>>> Please use the function 'listAttributes' to get valid attribute
names
>>>
>>> I am thus unable to reproduce previous results.
>>> Have no idea how this could happen, If anyone can help it will be
great.
>>> Thanks
>>> Konika
>>>
>>> _______________________________________________
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>>
>> --
>>
>>
>> Wolfgang Huber
>> EMBL
>> http://www.embl.de/research/units/genome_biology/huber
>>
>> _______________________________________________
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>
>