Search
Question: biomaRt getBM error
0
gravatar for array chip
12 weeks ago by
array chip350
array chip350 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!

 

ADD COMMENTlink modified 12 weeks ago • written 12 weeks ago by array chip350
0
gravatar for Mike Smith
12 weeks ago by
Mike Smith2.8k
EMBL Heidelberg / de.NBI
Mike Smith2.8k 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 12 weeks ago by Mike Smith2.8k
0
gravatar for array chip
12 weeks ago by
array chip350
array chip350 wrote:

Thanks Mike. Yes it worked with your code!

ADD COMMENTlink written 12 weeks ago by array chip350
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 2.2.0
Traffic: 258 users visited in the last hour