Hey everyone,

I'm trying to get gene names for a list of about 2k position on various chromosome I have.

The query I'm using is:

genes <- getBM(attributes=c('ensembl_gene_id', 'hgnc_symbol'), filters = c('chromosome_name', 'start', 'end'), values = list(chr, pos_start, pos_end), mart = ensembl)

But every time I get the same error:

Error in value[[3L]](cond) : 
  Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.

I've also tried to change to host, as so:

ensembl = useMart(host = 'grch37.ensembl.org', biomart='ENSEMBL_MART_ENSEMBL', dataset='hsapiens_gene_ensembl') 

But I'm still getting the same error.

Is it a problem on my end or is the server really down? Am I not using the query correctly?

Thanks

sessionInfo()

R version 3.2.3 (2015-12-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

locale:
[1] LC_COLLATE=Hebrew_Israel.1255  LC_CTYPE=Hebrew_Israel.1255    LC_MONETARY=Hebrew_Israel.1255 LC_NUMERIC=C                   LC_TIME=Hebrew_Israel.1255    

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

other attached packages:
[1] biomaRt_2.26.1      multtest_2.26.0     Biobase_2.30.0      BiocGenerics_0.16.1

loaded via a namespace (and not attached):
 [1] IRanges_2.4.6        XML_3.98-1.3         bitops_1.0-6         MASS_7.3-45          DBI_0.3.1            stats4_3.2.3         RSQLite_1.0.0        S4Vectors_0.8.7     
 [9] splines_3.2.3        tools_3.2.3          RCurl_1.95-4.7       survival_2.38-3      AnnotationDbi_1.32.3

Most likely it was just down. Have you tried again?

> library(biomaRt)
> ensembl = useMart(host = 'grch37.ensembl.org', biomart='ENSEMBL_MART_ENSEMBL', dataset='hsapiens_gene_ensembl')
> ensembl
Object of class 'Mart':
 Using the ENSEMBL_MART_ENSEMBL BioMart database
 Using the hsapiens_gene_ensembl dataset
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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] compiler_3.2.2       IRanges_2.4.6        parallel_3.2.2      
 [4] DBI_0.3.1            tools_3.2.2          RCurl_1.95-4.7      
 [7] Biobase_2.30.0       AnnotationDbi_1.32.3 RSQLite_1.0.0       
[10] S4Vectors_0.8.6      BiocGenerics_0.16.1  stats4_3.2.2        
[13] bitops_1.0-6         XML_3.98-1.3