[BioC] problem with biomaRt and mouse affy queries

[Wolfgang Huber]

Hi Vincent,

the following script worked for me, using a more recent version of 
biomaRt (1.7.1). I believe that Ensembl have renamed some of their gene 
attributes since the biomaRt package 1.6.0 (which you are using) was 
released, making the code in the getGene function invalid.

Not much we can do here - when the Ensembl people change their data 
names, we have to follow (but they tell us the pace of renaming will 
slow down now, since the most egregious mis-nomers of the past have been 
cleaned up.)

  Best, Wolfgang


library("biomaRt")
ids<-c("1415670_at","1415671_at","1415672_at","1415673_at",
        "1415674_a_at","1415675_at","1415676_a_at","1415677_at",
        "1415678_at","1415679_at")

m.mart <- useMart("ensembl", dataset = "mmusculus_gene_ensembl")

genes <- getGene(id = ids, array = "affy_mouse430_2", mart = m.mart)

 > genes[1:3, c(1:2,4:6)]
           ID   symbol chromosome band strand
1 1415671_at Atp6v0d1          8   D2     -1
2 1415672_at                   X          -1
3 1415672_at   Golga7          8   A3     -1





 > sessionInfo()
R version 2.4.0 Under development (unstable) (2006-06-27 r38431)
i686-pc-linux-gnu

locale:
LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"
[7] "base"

other attached packages:
  biomaRt    RCurl      XML fortunes
  "1.7.1"  "0.6-2" "0.99-7"  "1.2-1"


------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

---------------------------------------------------
> 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/
> 
> IRIBHM
> Bldg C, room C.4.116
> ULB, Campus Erasme, CP602
> 808 route de Lennik
> B-1070 Brussels
> Belgium
> 
> Phone: +32-2-555 4220
> Fax: +32-2-555 4655
>