On Wed, Apr 15, 2009 at 9:31 AM, Syed Haider <[email protected]> wrote:
> Hi Ruben,
>
> Have you tried executing your query getBM(...) with 'agilent_gf2519f' ?
> biomaRt throws exception in both case (agilent_gf2519f and agilent_gf2519F).
> The real attribute is 'agilent_gf2519f' which works fine from
> www.biomart.org. I am not sure how the new release is going to fix this
> bug, may be i am missing something here. By trying it on R, i feel that its
> a problem with R API of biomaRt, cc'ing Steffen who would know how to debug
> this.
>
>
Its a few years since I was involved with this but I have a feeling
BioConductor hard codes the names of attributes and filters you can use and
if these don't match the names in the EnsemblMart config then things break.
At least that used to be the case. So it seems either Rhoda has to change
the name back in the next ensembl release or the hard coded name in
BioConductor will need changing. Steffen will know more
Cheers
Damian
> Best,
> Syed
>
>
> Ruben wrote:
>
>> Hi Syed,
>>
>> in biomaRt from bioconductor the attribute name is 'agilent_g2519F'. If I
>> execute this code
>>
>> > ensembl = useMart("ensembl");
>> > ensembl = useDataset("drerio_gene_ensembl", mart=ensembl);
>> > atr <- listAttributes(ensembl)
>> > atr$name[3]
>>
>> I get this:
>>
>> > [1] "agilent_g2519F"
>>
>> It seems that there is a bug, but the new release will fix it.
>>
>> Thanks again,
>> Rubén.
>>
>>
>> Syed Haider wrote:
>>
>>> Ruben,
>>>
>>> the attribute name is: 'agilent_g2519f' not 'agilent_g2519F'
>>>
>>>
>>> hope this works.
>>>
>>> Best,
>>> Syed
>>>
>>>
>>> Rhoda Kinsella wrote:
>>>
>>>> Hi Ruben,
>>>> I suspect that there is inconsistency between the spelling of the
>>>> internal name of the filter and the attribute. I will look into it and try
>>>> to fix it for release 54 (approx end of April). Many apologies for any
>>>> inconvenience caused.
>>>> Regards,
>>>> Rhoda
>>>>
>>>>
>>>> On 14 Apr 2009, at 12:27, Ruben wrote:
>>>>
>>>> Hi to all,
>>>>>
>>>>> I am trying to invoke the following R code,
>>>>>
>>>>> ensembl = useMart("ensembl");
>>>>> ensembl = useDataset("drerio_gene_ensembl", mart=ensembl);
>>>>> ids <- getBM(attributes = c("ensembl_gene_id","agilent_g2519F"),
>>>>> filters = "with_agilent_g2519f", values =TRUE,mart=ensembl);
>>>>>
>>>>> but the result is always the same:
>>>>>
>>>>> 1 Query ERROR: caught BioMart::Exception::Usage: Attribute
>>>>> agilent_g2519F NOT FOUND
>>>>> Error en getBM(attributes = c("ensembl_gene_id", "agilent_g2519F"),
>>>>> filters = c("with_agilent_g2519f"), :
>>>>> Number of columns in the query result doesn't equal number of
>>>>> attributes in query. This is probably an internal error, please report.
>>>>>
>>>>> However, if I retrieve the list of available attributes I can see
>>>>> "agilent_g2519F" in the list.
>>>>>
>>>>> Can you help me? There is a mistake in my code or there is something
>>>>> wrong in biomart?
>>>>>
>>>>> Thanks in advance,
>>>>> Rubén.
>>>>>
>>>>
>>>> Rhoda Kinsella Ph.D.
>>>> Ensembl Bioinformatician,
>>>> European Bioinformatics Institute (EMBL-EBI),
>>>> Wellcome Trust Genome Campus,
>>>> Hinxton
>>>> Cambridge CB10 1SD,
>>>> UK.
>>>>
>>>
