Error in useMart while using a dataset in biomaRt
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Entering edit mode
clarisbaby • 0
@clarisbaby-14317
Last seen 6.6 years ago
Hey everyone,
I am trying to use C. elegans dataset available from biomaRt for annotation purpose. The commands I use runs at a given point of time and shows no error while the same command give error when run again. I have tried to run different variations for the same command, but each one has the same issue. 
Please guide me through, as I am trying to incorporate this command in one of the RNA-seq analysis package i am developing... 

the following is the codes i have used and the error messages received

1.
> m <- useMart(biomart="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", path="/biomart/martservice", dataset="celegans_gene_ensembl")
Error in checkDataset(dataset = dataset, mart = mart) : 
  The given dataset:  celegans_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets() function.
> m <- useMart(biomart="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", path="/biomart/martservice", dataset="celegans_gene_ensembl")
Error in checkDataset(dataset = dataset, mart = mart) : 
  The given dataset:  celegans_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets() function.
> m <- useMart(biomart="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", path="/biomart/martservice", dataset="celegans_gene_ensembl")

2.
> m <- biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "celegans_gene_ensembl", host = 'ensembl.org')
Error in checkDataset(dataset = dataset, mart = mart) : 
  The given dataset:  celegans_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets() function.
> m <- biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "celegans_gene_ensembl", host = 'ensembl.org')
3.
> m <- useMart("ensembl",dataset=("celegans_gene_ensembl"))
Error in checkDataset(dataset = dataset, mart = mart) : 
  The given dataset:  celegans_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets() function.
> m <- useMart("ensembl",dataset=("celegans_gene_ensembl"))
Error in checkDataset(dataset = dataset, mart = mart) : 
  The given dataset:  celegans_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets() function.
> m <- useMart("ensembl",dataset=("celegans_gene_ensembl"))
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_IN.UTF-8       LC_NUMERIC=C               LC_TIME=en_IN.UTF-8        LC_COLLATE=en_IN.UTF-8    
 [5] LC_MONETARY=en_IN.UTF-8    LC_MESSAGES=en_IN.UTF-8    LC_PAPER=en_IN.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] RNAseq_0.1.0               biomaRt_2.32.1             knitr_1.17                 Rqc_1.10.2                
 [5] ggplot2_2.2.1              GenomicFeatures_1.28.5     AnnotationDbi_1.38.2       systemPipeR_1.10.2        
 [9] ShortRead_1.34.1           GenomicAlignments_1.12.2   SummarizedExperiment_1.6.5 DelayedArray_0.2.7        
[13] matrixStats_0.52.2         Biobase_2.36.2             BiocParallel_1.10.1        Rsamtools_1.28.0          
[17] Biostrings_2.44.2          XVector_0.16.0             GenomicRanges_1.28.6       GenomeInfoDb_1.12.2       
[21] IRanges_2.10.4             S4Vectors_0.14.6           BiocGenerics_0.22.0       

loaded via a namespace (and not attached):
  [1] backports_1.1.1               GOstats_2.42.0                Hmisc_4.0-3                  
  [4] AnnotationHub_2.8.2           LSD_3.0                       plyr_1.8.4                   
  [7] lazyeval_0.2.0                GSEABase_1.38.2               splines_3.4.0                
 [10] BatchJobs_1.6                 easyRNASeq_2.12.1             digest_0.6.12                
 [13] BiocInstaller_1.26.1          ensembldb_2.0.4               htmltools_0.3.6              
 [16] GO.db_3.4.1                   gdata_2.18.0                  magrittr_1.5                 
 [19] checkmate_1.8.4               memoise_1.1.0                 BBmisc_1.11                  
 [22] BSgenome_1.44.2               cluster_2.0.6                 DEXSeq_1.22.0                
 [25] limma_3.32.7                  annotate_1.54.0               fail_1.3                     
 [28] colorspace_1.3-2              blob_1.1.0                    RCurl_1.95-4.8               
 [31] graph_1.54.0                  roxygen2_6.0.1                genefilter_1.58.1            
 [34] ape_4.1                       brew_1.0-6                    survival_2.41-3              
 [37] sendmailR_1.2-1               VariantAnnotation_1.22.3      gtable_0.2.0                 
 [40] zlibbioc_1.22.0               scales_0.5.0                  DESeq_1.28.0                 
 [43] vsn_3.44.0                    pheatmap_1.0.8                DBI_0.7                      
 [46] edgeR_3.18.1                  Rcpp_0.12.13                  xtable_1.8-2                 
 [49] htmlTable_1.9                 foreign_0.8-69                bit_1.1-12                   
 [52] preprocessCore_1.38.1         Formula_1.2-2                 intervals_0.15.1             
 [55] AnnotationForge_1.18.2        htmlwidgets_0.9               httr_1.3.1                   
 [58] gplots_3.0.1                  RColorBrewer_1.1-2            acepack_1.4.1                
 [61] reshape_0.8.7                 pkgconfig_2.0.1               XML_3.98-1.9                 
 [64] Gviz_1.20.0                   nnet_7.3-12                   locfit_1.5-9.1               
 [67] rlang_0.1.2                   reshape2_1.4.2                munsell_0.4.3                
 [70] tools_3.4.0                   qrqc_1.30.0                   RSQLite_2.0                  
 [73] devtools_1.13.3               evaluate_0.10.1               stringr_1.2.0                
 [76] yaml_2.1.14                   bit64_0.9-7                   caTools_1.17.1               
 [79] AnnotationFilter_1.0.0        ASpli_1.2.3                   nlme_3.1-131                 
 [82] RBGL_1.52.0                   mime_0.5                      xml2_1.1.1                   
 [85] genomeIntervals_1.32.0        BiocStyle_2.4.1               compiler_3.4.0               
 [88] curl_2.8.1                    interactiveDisplayBase_1.14.0 affyio_1.46.0                
 [91] tibble_1.3.4                  statmod_1.4.30                geneplotter_1.54.0           
 [94] stringi_1.1.5                 GenomicFiles_1.12.0           lattice_0.20-35              
 [97] ProtGenerics_1.8.0            Matrix_1.2-11                 commonmark_1.4               
[100] markdown_0.8                  data.table_1.10.4             bitops_1.0-6                 
[103] httpuv_1.3.5                  rtracklayer_1.36.5            affy_1.54.0                  
[106] R6_2.2.2                      latticeExtra_0.6-28           hwriter_1.3.2                
[109] KernSmooth_2.23-15            gridExtra_2.3                 dichromat_2.0-0              
[112] gtools_3.5.0                  DESeq2_1.16.1                 Category_2.42.1              
[115] rprojroot_1.2                 rjson_0.2.15                  withr_2.0.0                  
[118] GenomeInfoDbData_0.99.0       grid_3.4.0                    rpart_4.1-11                 
[121] rmarkdown_1.6                 biovizBase_1.24.0             shiny_1.0.5                  
[124] base64enc_0.1-3  

It would be very kind if anyone can suggest me where I am going wrong and how to use this command

Thanks in advance.

 

biomaRt bioconductor celegans annotation • 1.7k views
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Entering edit mode
Mike Smith ★ 6.6k
@mike-smith
Last seen 2 hours ago
EMBL Heidelberg

The c.elegans data is now available from http://metazoa.ensembl.org/ rather than standard www.ensembl.org.  Hence you have to use that in the host argument to useMart() e.g.

celegans_mart <- useMart(host = "metazoa.ensembl.org", 
                         biomart = "metazoa_mart",
                         dataset = "celegans_eg_gene")

You can then query it in the usual biomaRt way:

getBM(mart = celegans_mart,
      filters = "ensembl_gene_id",
      values = "WBGene00000001",
      attributes = c("ensembl_gene_id", "ensembl_transcript_id"))
  ensembl_gene_id ensembl_transcript_id
1  WBGene00000001          Y110A7A.10.1
2  WBGene00000001          Y110A7A.10.2

Did you get the version you're trying from an online tutorial?  If you did, and it's now out-of-date, I should try to update it to make sure it reflects how to do this correctly.

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Entering edit mode

Thanku so much @Mike Smith. The above stated command worked just fine and some of my packages do seem to be out-of-date, I will surely try and update them. Thanks for the suggestion too.

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