Which ever is the case, the name even if with small 'f' still is not the
same as with_*. What i see right now is that both att and filt have
small 'f'. I wonder where is the capital 'F' is coming from ?
wwe also need to be careful in changing names since other clients also
have saved queries which might break.
Syed
Damian Smedley wrote:
On Wed, Apr 15, 2009 at 9:31 AM, Syed Haider <[email protected]
<mailto:[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
<http://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.
