Question: biomaRt getBM error
0
gravatar for array chip
18 months ago by
array chip360
array chip360 wrote:

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 • 343 views
ADD COMMENTlink modified 18 months ago • written 18 months ago by array chip360
Answer: biomaRt getBM error
0
gravatar for Mike Smith
18 months ago by
Mike Smith4.0k
EMBL Heidelberg / de.NBI
Mike Smith4.0k wrote:

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)
ADD COMMENTlink written 18 months ago by Mike Smith4.0k
Answer: biomaRt getBM error
0
gravatar for array chip
18 months ago by
array chip360
array chip360 wrote:

Thanks Mike. Yes it worked with your code!

ADD COMMENTlink written 18 months ago by array chip360
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 302 users visited in the last hour