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!