[BioC] biomaRt error

[sdurinck at ebi.ac.uk]

Hi,

> My understanding is that the BioMart folks are making changes to the
> table names for the BioMart database, and this is happening right now
> (e.g, right after BioC 1.8 is released). Unfortunately this means that
> some of the convenience functions like getGene() are being broken.

This is correct however here there is a problem with the zebrafish dataset
as well.  Part of the error here is produced by an inconistency in
attribute and filter naming.  The attribute for the affyids is
zebrafish_affy and the filter is called affy_zebrafish.  The getGene
function expects these to have the same name and thus generates an error.

To make the BioMart datasets better we can post these inconsistencies to
the corresponding BioMart mailinglist (in this case the Ensembl helpdesk)
so they get fixed in the next database release.

Best,
Steffen

> Hi Georg,
>
> Georg Otto wrote:
>> Hi,
>>
>> using biomaRt, I get an error:
>>
>>
>>>mart<-useMart("ensembl", dataset= "drerio_gene_ensembl")
>>>getAffyArrays(mart)
>>
>> [1] "affy_zebrafish"
>>
>>>getGene(id=genes.regulated.mas5, array="affy_zebrafish" , mart=mart)
>>
>> Error in getBM(attributes = c(attrib, "hgnc_symbol", "description",
>> chrname,  :
>>         attribute: affy_zebrafish not found, please use the function
>> 'listAttributes' to get valid attribute names
>>
>>
>> Then I use listAttributes() as requested:
>>
>>
>>>listAttributes(mart=mart)
>>
>>
>> and get the following output:
>>
>> <snip>
>> [309] "zebrafish_affy"
>> [310] "zebrafish_affy_primary_db"
>> <snip>
>>
>> using "zebrafish_affy" instead of "affy_zebrafish" does not help,
>> however:
>>
>>
>>>getGene(id=genes.regulated.mas5, array="zebrafish_affy" , mart=mart)
>>
>> Error in getBM(attributes = c(attrib, "hgnc_symbol", "description",
>> chrname,  :
>>         attribute: hgnc_symbol not found, please use the function
>> 'listAttributes' to get valid attribute names
>>
>> Any hint will be appreciated.
>
> My understanding is that the BioMart folks are making changes to the
> table names for the BioMart database, and this is happening right now
> (e.g, right after BioC 1.8 is released). Unfortunately this means that
> some of the convenience functions like getGene() are being broken.
>
> I think your best bet is to use getBM() directly, and query for things
> that you see when you do listAttributes(mart).
>
> HTH,
>
> Jim
>
>
>>
>> Best,
>>
>> Georg
>>
>>
>>>sessionInfo()
>>
>>
>> Version 2.3.0 (2006-04-24)
>> powerpc-apple-darwin8.6.0
>>
>> attached base packages:
>> [1] "methods"   "stats"     "graphics"  "grDevices" "utils"
>> "datasets"
>> [7] "base"
>>
>> other attached packages:
>>  biomaRt    RCurl      XML
>>  "1.6.0"  "0.6-2" "0.99-7"
>>
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>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
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>
>
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