BiomaRt Error: "character string of length 1."
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coyoung ▴ 10
@coyoung-17963
Last seen 4.9 years ago

Hello I am having a issue with BioMart can anyone help.

I keep getting the error: The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1.

head(cleanDat.editrow[1:5,1:5])
rownames(cleanDat.editrow)
dim(cleanDat.editrow) #31391, 532
# mart=useMart('ensembl')
#tableSymbols<-getBM(attributes=c("hgnc_symbol","ensembl_gene_id"), filters="ensembl_gene_id", values=rownames(cleanDat),mart=human)
ensembl = useMart('ensembl', dataset='hsapiens_gene_ensembl', host = "www.ensembl.org", ensemblRedirect = FALSE)
genemap <- getBM(attributes = c('ensembl_gene_id', 'hgnc_symbol'), filters='ensembl_gene_id', values=rownames(cleanDat.editrow), mart=ensembl)

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] tidyr_1.0.0           boot_1.3-23           stringr_1.4.0         plotly_4.9.0          biomaRt_2.40.5        doParallel_1.0.15     iterators_1.0.12     
 [8] foreach_1.4.7         ggpubr_0.2.3          magrittr_1.5          gridExtra_2.3         reshape2_1.4.3        Cairo_1.5-10          RColorBrewer_1.1-2   
[15] ggplot2_3.2.1         igraph_1.2.4.1        NMF_0.21.0            Biobase_2.44.0        BiocGenerics_0.30.0   cluster_2.1.0         rngtools_1.4         
[22] pkgmaker_0.27         registry_0.5-1        WGCNA_1.68            fastcluster_1.1.25    dynamicTreeCut_1.63-1

loaded via a namespace (and not attached):
 [1] bitops_1.0-6          matrixStats_0.55.0    robust_0.4-18.1       fit.models_0.5-14     bit64_0.9-7           httr_1.4.1            progress_1.2.2       
 [8] tools_3.6.1           backports_1.1.5       R6_2.4.0              rpart_4.1-15          Hmisc_4.2-0           DBI_1.0.0             lazyeval_0.2.2       
[15] colorspace_1.4-1      nnet_7.3-12           withr_2.1.2           prettyunits_1.0.2     tidyselect_0.2.5      curl_4.2              bit_1.1-14           
[22] compiler_3.6.1        preprocessCore_1.46.0 htmlTable_1.13.2      xml2_1.2.2            scales_1.0.0          checkmate_1.9.4       DEoptimR_1.0-8       
[29] mvtnorm_1.0-11        robustbase_0.93-5     digest_0.6.22         foreign_0.8-72        rrcov_1.4-7           base64enc_0.1-3       pkgconfig_2.0.3      
[36] htmltools_0.4.0       bibtex_0.4.2          htmlwidgets_1.5.1     rlang_0.4.1           rstudioapi_0.10       RSQLite_2.1.2         impute_1.58.0        
[43] jsonlite_1.6          acepack_1.4.1         dplyr_0.8.3           RCurl_1.95-4.12       GO.db_3.8.2           Formula_1.2-3         Matrix_1.2-17        
[50] Rcpp_1.0.2            munsell_0.5.0         S4Vectors_0.22.1      lifecycle_0.1.0       stringi_1.4.3         MASS_7.3-51.4         plyr_1.8.4           
[57] grid_3.6.1            blob_1.2.0            crayon_1.3.4          lattice_0.20-38       splines_3.6.1         hms_0.5.1             zeallot_0.1.0        
[64] knitr_1.25            pillar_1.4.2          ggsignif_0.6.0        codetools_0.2-16      stats4_3.6.1          XML_3.98-1.20         glue_1.3.1           
[71] latticeExtra_0.6-28   BiocManager_1.30.9    data.table_1.12.6     vctrs_0.2.0           gtable_0.3.0          purrr_0.3.3           assertthat_0.2.1     
[78] xfun_0.10             gridBase_0.4-7        xtable_1.8-4          viridisLite_0.3.0     survival_2.44-1.1     pcaPP_1.9-73          tibble_2.1.3         
[85] AnnotationDbi_1.46.1  memoise_1.1.0         IRanges_2.18.3
biomaRt • 442 views
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swbarnes2 ★ 1.4k
@swbarnes2-14086
Last seen 1 day ago
San Diego

The biomart-based lines of the code work for me

ensembl = useMart('ensembl', dataset='hsapiens_gene_ensembl', host = "www.ensembl.org", ensemblRedirect = FALSE)
genemap <- getBM(attributes = c('ensembl_gene_id', 'hgnc_symbol'), filters='ensembl_gene_id', values='ENSG00000000003', mart=ensembl)
genemap
  ensembl_gene_id hgnc_symbol
1 ENSG00000000003      TSPAN6

Your list of gene IDs must be flawed.

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Or, it could be a transient problem at the Biomart server, for which using useEnsembl and choosing a close mirror may help.

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