Hi Syed,
The problem is that biomaRt relies on the internal name for filters
and corresponding internal name attributes to be the same. In this
case the internal name for the attribute has an uppercase F instead of
a lower case one and so it throws an error. I have changed this in the
config and hopefully this will solve the problem for release 54.
Regards,
Rhoda
On 15 Apr 2009, at 09:31, Syed Haider 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.
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.
Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.
