Hi all,

I'm seeing the following error when using the getGene() function in the biomaRt package. Can anyone please help?

> library(biomaRt)
> example(getGene)

getGen> if(interactive()){
getGen+ 
getGen+ mart = useMart("ensembl", dataset="hsapiens_gene_ensembl")
getGen+ 
getGen+ #example using affy id
getGen+ 
getGen+ g = getGene( id = "1939_at", type = "affy_hg_u95av2", mart = mart)
getGen+ show(g)
getGen+ 
getGen+ #example using Entrez Gene id
getGen+ 
getGen+ g = getGene( id = "100", type = "entrezgene", mart = mart)
getGen+ show(g)
getGen+ }
Error in martCheck(mart, "ensembl") : 
  This function only works when used with the ensembl BioMart.
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] biomaRt_2.26.1

loaded via a namespace (and not attached):
 [1] IRanges_2.4.4        tools_3.2.2          parallel_3.2.2      
 [4] DBI_0.3.1            RCurl_1.95-4.7       Biobase_2.30.0      
 [7] AnnotationDbi_1.32.0 RSQLite_1.0.0        S4Vectors_0.8.3     
[10] BiocGenerics_0.16.1  stats4_3.2.2         bitops_1.0-6        
[13] XML_3.98-1.3      

Hello,

If you replace:

mart = useMart("ensembl", dataset="hsapiens_gene_ensembl")

with

mart = useMart(biomart="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", path="/biomart/martservice", dataset="hsapiens_gene_ensembl")

or

mart = useEnsembl(biomart="ensembl",dataset="hsapiens_gene_ensembl")

it should work.

Hope this helps,

Thomas