Ensembl sheep dataset in biomaRt
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Entering edit mode
@pokharelkisun-9612
Last seen 5.7 years ago

Hi,

I have not been able to load latest sheep datasets using biomaRt. The following is the line of code I used: 

ensembl<-useDataset(dataset = "oaries_gene_ensembl", mart = ensembl)

 

and the following is the error message:

Error in checkDataset(dataset = dataset, mart = mart) : The given dataset: oaries_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets() function.

session info

> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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

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

other attached packages:
 [1] gplots_3.0.1               RColorBrewer_1.1-2        
 [3] BiocParallel_1.10.1        DESeq2_1.16.1             
 [5] SummarizedExperiment_1.6.5 DelayedArray_0.2.7        
 [7] matrixStats_0.54.0         Biobase_2.36.2            
 [9] GenomicRanges_1.28.6       GenomeInfoDb_1.12.3       
[11] IRanges_2.10.5             S4Vectors_0.14.7          
[13] BiocGenerics_0.22.1        biomaRt_2.32.1            

loaded via a namespace (and not attached):
 [1] bitops_1.0-6            bit64_0.9-7            
 [3] tools_3.4.4             backports_1.1.2        
 [5] R6_2.2.2                KernSmooth_2.23-15     
 [7] rpart_4.1-13            Hmisc_4.1-1            
 [9] DBI_1.0.0               lazyeval_0.2.1         
[11] colorspace_1.3-2        nnet_7.3-12            
[13] tidyselect_0.2.4        gridExtra_2.3          
[15] bit_1.1-14              compiler_3.4.4         
[17] htmlTable_1.12          caTools_1.17.1.1       
[19] scales_1.0.0            checkmate_1.8.5        
[21] genefilter_1.58.1       stringr_1.3.1          
[23] digest_0.6.15           foreign_0.8-69         
[25] DOSE_3.2.0              XVector_0.16.0         
[27] base64enc_0.1-3         pkgconfig_2.0.1        
[29] htmltools_0.3.6         htmlwidgets_1.2        
[31] rlang_0.2.1             rstudioapi_0.7         
[33] RSQLite_2.1.1           bindr_0.1.1            
[35] gtools_3.8.1            acepack_1.4.1          
[37] GOSemSim_2.2.0          dplyr_0.7.6            
[39] RCurl_1.95-4.11         magrittr_1.5           
[41] GO.db_3.4.1             GenomeInfoDbData_0.99.0
[43] Formula_1.2-3           Matrix_1.2-12          
[45] Rcpp_0.12.18            munsell_0.5.0          
[47] yaml_2.2.0              stringi_1.2.4          
[49] zlibbioc_1.22.0         plyr_1.8.4             
[51] qvalue_2.8.0            grid_3.4.4             
[53] blob_1.1.1              gdata_2.18.0           
[55] DO.db_2.9               crayon_1.3.4           
[57] lattice_0.20-35         splines_3.4.4          
[59] annotate_1.54.0         locfit_1.5-9.1         
[61] knitr_1.20              pillar_1.3.0           
[63] fgsea_1.2.1             igraph_1.2.2           
[65] geneplotter_1.54.0      reshape2_1.4.3         
[67] fastmatch_1.1-0         XML_3.98-1.15          
[69] glue_1.3.0              latticeExtra_0.6-28    
[71] data.table_1.11.4       gtable_0.2.0           
[73] purrr_0.2.5             tidyr_0.8.1            
[75] assertthat_0.2.0        ggplot2_3.0.0          
[77] xtable_1.8-2            survival_2.41-3        
[79] tibble_1.4.2            clusterProfiler_3.4.4  
[81] rvcheck_0.1.0           AnnotationDbi_1.38.2   
[83] memoise_1.1.0           bindrcpp_0.2.2         
[85] cluster_2.0.6<font face="sans-serif, Arial, Verdana, Trebuchet MS">
</font>
ensembl biomart oaries • 960 views
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Entering edit mode

Edit: Now, it's working - I don't know how.

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Entering edit mode
Mike Smith ★ 6.5k
@mike-smith
Last seen 7 hours ago
EMBL Heidelberg

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 are seeing. See A: biomaRt: drerio_gene_ensembl dataset missing  or https://www.biostars.org/p/289654/#289861 for more details.

You are currently using old versions of both R and biomaRt. I would suggest updating both, in particular you will need biomaRt version 2.34.1 or newer to handle this correctly.

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