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.
