biomaRt getBM error
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0
Entering edit mode
array chip ▴ 420
@array-chip-4136
Last seen 11 weeks ago
United States

Hi, I am getting this error today. It worked just last week. can anyone suggest what's going on?

> library(biomaRt)

> ensembl=useMart("ensembl")
> ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)

> getBM(attributes=c('hgnc_symbol', 'ensembl_gene_id', 'entrezgene','description'), 
  filters = 'ensembl_gene_id', values="ENSG00000172350", mart = ensembl)

Error in getBM(attributes = c("hgnc_symbol", "ensembl_gene_id", "entrezgene",  : 
  The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this to the mailing list.

 

> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

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

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] xml2_1.2.0                 biomaRt_2.34.2             DESeq2_1.18.1              SummarizedExperiment_1.8.1
 [5] DelayedArray_0.4.1         matrixStats_0.53.1         Biobase_2.38.0             GenomicRanges_1.30.3      
 [9] GenomeInfoDb_1.14.0        IRanges_2.12.0             S4Vectors_0.16.0           BiocGenerics_0.24.0       

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.16           locfit_1.5-9.1         lattice_0.20-35        prettyunits_1.0.2      assertthat_0.2.0      
 [6] digest_0.6.15          R6_2.2.2               plyr_1.8.4             backports_1.1.2        acepack_1.4.1         
[11] RSQLite_2.1.0          httr_1.3.1             ggplot2_2.2.1          pillar_1.2.1           zlibbioc_1.24.0       
[16] rlang_0.2.0            progress_1.1.2         curl_3.2               lazyeval_0.2.1         rstudioapi_0.7        
[21] data.table_1.10.4-3    annotate_1.56.2        blob_1.1.1             rpart_4.1-13           Matrix_1.2-14         
[26] checkmate_1.8.5        splines_3.4.4          BiocParallel_1.12.0    geneplotter_1.56.0     stringr_1.3.0         
[31] foreign_0.8-69         htmlwidgets_1.0        RCurl_1.95-4.10        bit_1.1-12             munsell_0.4.3         
[36] compiler_3.4.4         base64enc_0.1-3        htmltools_0.3.6        nnet_7.3-12            tibble_1.4.2          
[41] gridExtra_2.3          htmlTable_1.11.2       GenomeInfoDbData_1.0.0 Hmisc_4.1-1            XML_3.98-1.10         
[46] bitops_1.0-6           grid_3.4.4             xtable_1.8-2           gtable_0.2.0           DBI_0.8               
[51] magrittr_1.5           scales_0.5.0           stringi_1.1.7          XVector_0.18.0         genefilter_1.60.0     
[56] latticeExtra_0.6-28    Formula_1.2-2          RColorBrewer_1.1-2     tools_3.4.4            bit64_0.9-7           
[61] survival_2.42-3        AnnotationDbi_1.40.0   colorspace_1.3-2       cluster_2.0.7-1        memoise_1.1.0         
[66] knitr_1.20 

Thank you!

 

biomart • 773 views
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0
Entering edit mode
Mike Smith ★ 6.5k
@mike-smith
Last seen 58 minutes ago
EMBL Heidelberg

If you are in the United States then it seems that the local mirror is currently down, which may be why your query is failing (you can check by visiting http://uswest.ensembl.org)

You can try to force accessing the main site by using

ensembl = useMart(biomart = "ensembl", 
                  host = "www.ensembl.org", 
                  ensemblRedirect = FALSE)

ensembl = useDataset("hsapiens_gene_ensembl",
                     mart=ensembl)
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0
Entering edit mode
array chip ▴ 420
@array-chip-4136
Last seen 11 weeks ago
United States

Thanks Mike. Yes it worked with your code!

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