The support.bioconductor.org editor has been updated to markdown! Please see more info at: Tutorial: Updated Support Site Editor

Question: Error in useMart while using a dataset in biomaRt
0
gravatar for clarisbaby
13 months ago by
clarisbaby0
clarisbaby0 wrote:
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.

 

ADD COMMENTlink modified 13 months ago by Mike Smith3.2k • written 13 months ago by clarisbaby0
Answer: Error in useMart while using a dataset in biomaRt
0
gravatar for Mike Smith
13 months ago by
Mike Smith3.2k
EMBL Heidelberg / de.NBI
Mike Smith3.2k wrote:

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.

ADD COMMENTlink modified 13 months ago • written 13 months ago by Mike Smith3.2k

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.

ADD REPLYlink written 13 months ago by clarisbaby0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 271 users visited in the last hour