getLDS error in scan
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mvis1231 • 0
@mvis1231-24351
Last seen 11 months ago

Hi,

I have been trying to convert mouse gene symbols to human gene symbols using biomaRt. To do so, I am running this demo code first:

library(biomaRt)
human = useMart("ensembl", dataset = "hsapiens_gene_ensembl", host = "www.ensembl.org")
mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl", host = "www.ensembl.org")
genes = c("Zfp286", "Tmx2")
genes = getLDS(attributes = c("mgi_symbol"), filters = "mgi_symbol", values = genes ,mart = mouse, attributesL = c("hgnc_symbol","chromosome_name", "start_position"), martL = human, uniqueRows=T)

Unfortunately, I keep getting this error when I run getLDS:

Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 1 did not have 3 elements

Also for your information, when I tried to approach with version and to see what version was available by running listEnsemblArchives(), I also see this error:

Error: failed to load external entity "http://www.ensembl.org/info/website/archives/index.html?redirect=no"

Could you please advise me how to fix error? It will be much appreciated. (I posted the same question in GitHub (https://github.com/grimbough/biomaRt/issues/29) as well yesterday. I will remove one, once I get a support! Thank you for your understandings in advance)

The session info is:

R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

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

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] biomaRt_2.42.1              cowplot_1.1.0               SingleCellExperiment_1.8.0 
 [4] SingleR_1.0.6               SummarizedExperiment_1.16.1 DelayedArray_0.12.3        
 [7] BiocParallel_1.20.1         matrixStats_0.56.0          Biobase_2.46.0             
[10] GenomicRanges_1.38.0        GenomeInfoDb_1.22.1         IRanges_2.20.2             
[13] S4Vectors_0.24.4            BiocGenerics_0.32.0         ggplot2_3.3.2              
[16] patchwork_1.0.1             dplyr_1.0.0                 Seurat_3.2.1               
[19] bdsmatrix_1.3-4            

loaded via a namespace (and not attached):

  [1] AnnotationHub_2.18.0          BiocFileCache_1.10.2          plyr_1.8.6                   
  [4] igraph_1.2.5                  lazyeval_0.2.2                splines_3.6.3                
  [7] listenv_0.8.0                 digest_0.6.25                 htmltools_0.5.0              
 [10] magrittr_1.5                  memoise_1.1.0                 tensor_1.5                   
 [13] cluster_2.1.0                 ROCR_1.0-11                   globals_0.13.1               
 [16] askpass_1.1                   prettyunits_1.1.1             colorspace_1.4-1             
 [19] blob_1.2.1                    rappdirs_0.3.1                ggrepel_0.8.2                
 [22] xfun_0.17                     crayon_1.3.4                  RCurl_1.98-1.2               
 [25] jsonlite_1.7.1                spatstat_1.64-1               spatstat.data_1.4-3          
 [28] survival_3.1-8                zoo_1.8-8                     glue_1.4.0                   
 [31] polyclip_1.10-0               gtable_0.3.0                  zlibbioc_1.32.0              
 [34] XVector_0.26.0                leiden_0.3.3                  future.apply_1.6.0           
 [37] abind_1.4-5                   scales_1.1.1                  DBI_1.1.0                    
 [40] miniUI_0.1.1.1                Rcpp_1.0.4.6                  viridisLite_0.3.0            
 [43] xtable_1.8-4                  progress_1.2.2                reticulate_1.16              
 [46] bit_4.0.4                     rsvd_1.0.3                    htmlwidgets_1.5.2            
 [49] httr_1.4.2                    RColorBrewer_1.1-2            ellipsis_0.3.0               
 [52] ica_1.0-2                     pkgconfig_2.0.3               XML_3.99-0.3                 
 [55] uwot_0.1.8                    dbplyr_1.4.4                  deldir_0.1-28                
 [58] tidyselect_1.1.0              rlang_0.4.6                   reshape2_1.4.4               
 [61] later_1.1.0.1                 AnnotationDbi_1.48.0          munsell_0.5.0                
 [64] BiocVersion_3.10.1            tools_3.6.3                   generics_0.0.2               
 [67] RSQLite_2.2.0                 ExperimentHub_1.12.0          ggridges_0.5.2               
 [70] stringr_1.4.0                 fastmap_1.0.1                 yaml_2.2.1                   
 [73] goftest_1.2-2                 knitr_1.30                    bit64_4.0.5                  
 [76] fitdistrplus_1.1-1            purrr_0.3.4                   RANN_2.6.1                   
 [79] pbapply_1.4-3                 future_1.19.1                 nlme_3.1-144                 
 [82] mime_0.9                      compiler_3.6.3                rstudioapi_0.11              
 [85] plotly_4.9.2.1                curl_4.3                      png_0.1-7                    
 [88] interactiveDisplayBase_1.24.0 spatstat.utils_1.17-0         tibble_3.0.1                 
 [91] stringi_1.4.6                 lattice_0.20-38               Matrix_1.2-18                
 [94] vctrs_0.3.1                   pillar_1.4.6                  lifecycle_0.2.0              
 [97] BiocManager_1.30.10           lmtest_0.9-38                 RcppAnnoy_0.0.16             
[100] BiocNeighbors_1.4.2           data.table_1.12.8             bitops_1.0-6                 
[103] irlba_2.3.3                   httpuv_1.5.4                  R6_2.4.1                     
[106] promises_1.1.1                KernSmooth_2.23-16            gridExtra_2.3                
[109] codetools_0.2-16              MASS_7.3-51.5                 assertthat_0.2.1             
[112] openssl_1.4.2                 withr_2.3.0                   sctransform_0.2.1            
[115] GenomeInfoDbData_1.2.2        mgcv_1.8-31                   hms_0.5.3                    
[118] grid_3.6.3                    rpart_4.1-15                  tidyr_1.1.2                  
[121] DelayedMatrixStats_1.8.0      Rtsne_0.15                    shiny_1.5.0
biomaRt getLDS convert gene symbols • 511 views
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I'm actually getting the same error. Possible issue with the database?

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Mike Smith ★ 5.1k
@mike-smith
Last seen 1 day ago
EMBL Heidelberg / de.NBI

First, you're going to need to update to the latest version of biomaRt, and since you're using an old version of R we'll need to get that from GitHub with

BiocManager::install('grimbough/biomaRt')

Then create the two mart objects with useEnsembl()

human = useEnsembl("ensembl", dataset = "hsapiens_gene_ensembl")
mouse = useEnsembl("ensembl", dataset = "mmusculus_gene_ensembl")

I only have access to a phone right now, so can't run that code, but does that solve it?

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Hi Mike, Thank you so so much for your prompt support! Now it works very well. Thank you once again for your help.

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Just one more simple question, Mike. Does the useEnsembl() give us GRCh38 as default for both mouse and human?

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ensembl <- useEnsembl(biomart = "ensembl")
searchDatasets(mart = ensembl, pattern = "sapiens|musculus")

Returns the current genomic build for human and mouse

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Yes, useEnsembl() will use the most recent Ensembl version by default, so for humans that's currently GRCh38. @bioresearchg's code shows you how to list the builds that a specific mart object will access for various species.

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