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
>
