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coyoung
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@coyoung-17963
Last seen 4.8 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
Or, it could be a transient problem at the Biomart server, for which using
useEnsembl
and choosing a close mirror may help.