Question: BiomaRt - hsapiens dataset from Ensembl_Mart_Ensembl not recognised by R
0
gravatar for alisha.aman
10 months ago by
alisha.aman0 wrote:

Hi,

I cannot seem to use the homo sapiens dataset for ensembl gene annotation. While using useEnsembl('ensembl', dataset='hspaiens_gene_ensembl') command (or even it's variations), R just shows an error: Error in useDataset(mart = mart, dataset = dataset, verbose = verbose) : 
  The given dataset:  hspaiens_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets function

II have used this command before and it was working just fine. When using the listDatasets function, the dataset for humans was displayed as: thspaiens_gene_ensembl. I had tried using this dataset name as well but it failed. The other datasets work just fine, however. 

 

session info:

R version 3.3.3 (2017-03-06)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                            LC_TIME=English_United Kingdom.1252    

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

other attached packages:
 [1] ggplot2_2.2.1              DESeq2_1.14.1              SummarizedExperiment_1.4.0 Biobase_2.34.0            
 [5] GenomicRanges_1.26.4       GenomeInfoDb_1.10.3        IRanges_2.8.2              S4Vectors_0.12.2          
 [9] BiocGenerics_0.20.0        tidyr_0.8.0                purrr_0.2.4                dplyr_0.7.4               
[13] biomaRt_2.30.0            

loaded via a namespace (and not attached):
 [1] bit64_0.9-7          splines_3.3.3        Formula_1.2-2        assertthat_0.2.0     latticeExtra_0.6-28  blob_1.1.1          
 [7] pillar_1.2.1         RSQLite_2.1.0        backports_1.1.2      lattice_0.20-35      glue_1.2.0           digest_0.6.14       
[13] RColorBrewer_1.1-2   XVector_0.14.1       checkmate_1.8.5      colorspace_1.3-2     htmltools_0.3.6      Matrix_1.2-8        
[19] plyr_1.8.4           XML_3.98-1.11        pkgconfig_2.0.1      genefilter_1.56.0    zlibbioc_1.20.0      xtable_1.8-2        
[25] scales_0.5.0         BiocParallel_1.8.2   htmlTable_1.11.2     tibble_1.4.2         annotate_1.52.1      nnet_7.3-12         
[31] lazyeval_0.2.1       survival_2.42-3      magrittr_1.5         memoise_1.1.0        foreign_0.8-67       tools_3.3.3         
[37] data.table_1.10.4-3  stringr_1.3.0        munsell_0.4.3        locfit_1.5-9.1       cluster_2.0.5        AnnotationDbi_1.36.2
[43] bindrcpp_0.2.2       rlang_0.2.0          grid_3.3.3           RCurl_1.95-4.10      rstudioapi_0.7       htmlwidgets_1.0     
[49] bitops_1.0-6         base64enc_0.1-3      gtable_0.2.0         DBI_0.8              R6_2.2.2             gridExtra_2.3       
[55] knitr_1.20           bit_1.1-12           bindr_0.1.1          Hmisc_4.1-1          stringi_1.1.7        Rcpp_0.12.16        
[61] geneplotter_1.52.0   rpart_4.1-10         acepack_1.4.1   

 

 

 

 

 

biomart • 180 views
ADD COMMENTlink modified 10 months ago by Mike Smith3.3k • written 10 months ago by alisha.aman0
Answer: BiomaRt - hsapiens dataset from Ensembl_Mart_Ensembl not recognised by R
1
gravatar for James W. MacDonald
10 months ago by
United States
James W. MacDonald49k wrote:

You have a typo. I believe you want hsapiens_gene_ensembl, not hspaiens_gene_ensembl

ADD COMMENTlink written 10 months ago by James W. MacDonald49k
Answer: BiomaRt - hsapiens dataset from Ensembl_Mart_Ensembl not recognised by R
0
gravatar for Mike Smith
10 months ago by
Mike Smith3.3k
EMBL Heidelberg / de.NBI
Mike Smith3.3k wrote:

James is totally correct that you've got a typo in the dataset name, but I also wonder if you're experiencing the issue described in biomaRt: drerio_gene_ensembl dataset missing which would produce a similar error.

This was caused by the Ensembl release at that time including some species with apostrophes in their name for the first time, which broke listDatasets() so some entires couldn't be found even if spelt correctly.

I suggest updating your version of biomaRt to at least 2.34.1 where a patch was introduced.  You can do this via:

BiocInstaller::biocLite('biomaRt')
ADD COMMENTlink modified 10 months ago • written 10 months ago by Mike Smith3.3k
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