biomaRt rnorvegicus_gene_ensembl dataset is not valid!
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Entering edit mode
6.0 years ago
biocyberman ▴ 860

Accessing to rat dataset is unstable during last few days. Sometimes it works, sometimes I get error like the following (R code):

library(biomaRt)
human = useEnsembl("ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl") # works fine
rat = useEnsembl("ENSEMBL_MART_ENSEMBL", dataset = "rnorvegicus_gene_ensembl") # Error!
Error in checkDataset(dataset = dataset, mart = mart) : 
  The given dataset:  rnorvegicus_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets() function.

Update: Problem seems gone after I updated all bioconductor packages to 3.6. Will come back if it happens again.

Here is session info. I also tried yesterday with biomartian and faced the same problem.

sessionInfo() R version 3.4.4 (2018-03-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.4 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8   
 [6] LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] biomaRt_2.34.2       AnnotationHub_2.10.1 BiocGenerics_0.24.0  vimcom_1.2-5         setwidth_1.0-4       colorout_1.1-0      

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.8.1    progress_1.2.0                lattice_0.20-35               htmltools_0.3.6               stats4_3.4.4                 
 [6] rtracklayer_1.38.3            yaml_2.1.19                   interactiveDisplayBase_1.16.0 blob_1.1.1                    XML_3.98-1.11                
[11] rlang_0.2.1                   later_0.7.3                   DBI_1.0.0                     BiocParallel_1.12.0           bit64_0.9-7                  
[16] matrixStats_0.53.1            GenomeInfoDbData_1.0.0        stringr_1.3.1                 zlibbioc_1.24.0               Biostrings_2.46.0            
[21] memoise_1.1.0                 Biobase_2.38.0                IRanges_2.12.0                httpuv_1.4.4.2                GenomeInfoDb_1.14.0          
[26] BiocInstaller_1.28.0          AnnotationDbi_1.40.0          Rcpp_0.12.17                  xtable_1.8-2                  promises_1.0.1               
[31] DelayedArray_0.4.1            S4Vectors_0.16.0              XVector_0.18.0                mime_0.5                      bit_1.1-14                   
[36] Rsamtools_1.30.0              hms_0.4.2                     digest_0.6.15                 stringi_1.2.3                 shiny_1.1.0                  
[41] GenomicRanges_1.30.3          grid_3.4.4                    tools_3.4.4                   bitops_1.0-6                  magrittr_1.5                 
[46] RCurl_1.95-4.10               RSQLite_2.1.1                 crayon_1.3.4                  pkgconfig_2.0.1               Matrix_1.2-14                
[51] prettyunits_1.0.2             assertthat_0.2.0              httr_1.3.1                    rstudioapi_0.7                R6_2.2.2                     
[56] GenomicAlignments_1.14.2      compiler_3.4.4
biomaRt • 3.7k views
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Can you update your post to include the output of the command sessionInfo() so we can see what version of R & biomaRt you are using?

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Update: Problem seems gone after I updated all bioconductor packages to 3.6.

Post that as an answer and then accept it to provide closure to this thread.

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I will wait a few days to confirm. Not feel like to provide an uncertain answer with 'seems' :)

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Reason @Mike Smith asked you that question was he would have asked you to upgrade to the latest. What version of biomaRt were you on before (just for the record).

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I was using bioconductor version 3.5. I did not notice version of biomaRt.

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6.0 years ago
Mike Smith ★ 2.1k

There was an issue with biomaRt that manifested when Ensembl release 91 introduced datasets with apostrophes in e.g. "Ma's Night Monkey" which would lead to the error you were seeing. See https://support.bioconductor.org/p/104025/#104043 or A: biomaRt mmusculus_gene_ensembl dataset

If you were still using Bioconductor 3.5 and the associated version of biomaRt then this was likely the cause of the error you were seeing. Updating to biomaRt version 2.34.1 or newer should handle this correctly.

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