[BioC] problem with biomaRt and mouse affy queries

[Steffen Durinck]

Hi Vincent,

This is due to a recent change in Ensembl which makes getGene fail for 
any organism different than hsapiens.  A fix for biomaRt will be 
available later this week.  For now use the more general getBM function 
to retrieve the specific information you need.

best,
Steffen

Vincent Detours wrote:
> Dear all,
>
> Trying to reproduce the example in the biomaRt vignette using a mouse  
> instead of
> a human Affy array I sumbled on the following:
>
>  > ids
> [1] "1415670_at"   "1415671_at"   "1415672_at"   "1415673_at"    
> "1415674_a_at"
> [6] "1415675_at"   "1415676_a_at" "1415677_at"   "1415678_at"    
> "1415679_at"
>  > m.mart <- useMart("ensembl", dataset = "mmusculus_gene_ensembl")
> Checking attributes and filters ... ok
>  > genes <- getGene(id = ids, array = "affy_mouse430_2", mart = m.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 idea of what goes wrong?
> Note that the vignette example does work on my system (not shown).
> A query BioMart query (http://www.ensembl.org/Multi/martview) with
> the same probes and array type did work as well .
>
> I am using the following software versions
>  > sessionInfo()
> Version 2.3.1 RC (2006-05-30 r38234)
> powerpc-apple-darwin8.6.0
>
> attached base packages:
> [1] "splines"   "tools"     "methods"   "stats"     "graphics"   
> "grDevices"
> [7] "utils"     "datasets"  "base"
>
> other attached packages:
>         biomaRt          RCurl            XML           MASS  
> mouse4302probe
>         "1.6.0"        "0.6-2"       "0.99-7"     "7.2-27.1"        
> "1.12.0"
>    mouse4302cdf       annotate      mouse4302          gcrma     
> matchprobes
>        "1.12.0"       "1.10.0"       "1.12.0"        "2.4.1"         
> "1.4.0"
>            affy         affyio        Biobase
>        "1.10.0"        "1.0.0"       "1.10.0"
>  >
>
> Thanks in advance for your help.
> Best wishes to all,
>
> Vincent Detours, Ph. D.
> http://homepages.ulb.ac.be/~vdetours/
>
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