[BioC] biomaRt error

[James W. MacDonald]

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
734-647-5623


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