BiomaRt Error: "character string of length 1."
1
0
Entering edit mode
coyoung ▴ 10
@coyoung-17963
Last seen 4.4 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 • 360 views
ADD COMMENT
0
Entering edit mode
swbarnes2 ★ 1.4k
@swbarnes2-14086
Last seen 5 minutes 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.

ADD COMMENT
1
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1641 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6