Hi,

I've been using the following code in order to get gene names etc from ensembl based on a list of ensembl IDs from a sequencing experiment, and it has previously been running without issue.

mart <- useMart(biomart = "ensembl", dataset = "rnorvegicus_gene_ensembl")

genes_biomart <- getBM(attributes = c("ensembl_gene_id", "external_gene_name", "entrezgene"),

                                   filters = "ensembl_gene_id",

                                   values = geneid$`rownames(x)`, # column in df of ensembl IDs from RNA seq

                                  mart = mart)

However, since Friday (24/05) I have been getting the following error when running getBM

Batch submitting query [================>-------------------------------------------------]  26% eta: 17mError in getBM(attributes = c("ensembl_gene_id", "external_gene_name",  : 

The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. 
Please report this on the support site at http://support.bioconductor.org

I have tried changing the attributes I am calling in, and have changed it so I'm only asking for one of the attributes but I still get this error.

Session info:

> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

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

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

other attached packages:
[1] RColorBrewer_1.1-2 Glimma_1.12.0      biomaRt_2.40.0     stringr_1.4.0      dplyr_0.8.1       
[6] edgeR_3.26.4       limma_3.40.2      

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1           pillar_1.4.1         compiler_3.6.0       BiocManager_1.30.4   prettyunits_1.0.2   
 [6] progress_1.2.2       bitops_1.0-6         tools_3.6.0          digest_0.6.19        bit_1.1-14          
[11] jsonlite_1.6         RSQLite_2.1.1        memoise_1.1.0        tibble_2.1.1         lattice_0.20-38     
[16] pkgconfig_2.0.2      rlang_0.3.4          DBI_1.0.0            rstudioapi_0.10      curl_3.3            
[21] parallel_3.6.0       xml2_1.2.0           httr_1.4.0           hms_0.4.2            IRanges_2.18.0      
[26] S4Vectors_0.22.0     locfit_1.5-9.1       stats4_3.6.0         bit64_0.9-7          grid_3.6.0          
[31] tidyselect_0.2.5     glue_1.3.1           Biobase_2.44.0       R6_2.4.0             AnnotationDbi_1.46.0
[36] XML_3.98-1.19        purrr_0.3.2          blob_1.1.1           magrittr_1.5         BiocGenerics_0.30.0 
[41] assertthat_0.2.1     stringi_1.4.3        RCurl_1.95-4.12      crayon_1.3.4  

Any help is much appreciated!

Natalie

You can try querying one of the Ensembl mirrors which may be more responsive for you e.g.

mart <- useEnsembl(biomart = "ensembl", 
                   dataset = "rnorvegicus_gene_ensembl", 
                   mirror = "useast")

Values for the mirror argument are: useast, uswest, asia