Question: Ensembl sheep dataset in biomaRt
0
gravatar for pokharel.kisun
13 months ago by
pokharel.kisun0 wrote:

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>
biomart ensembl oaries • 255 views
ADD COMMENTlink modified 13 months ago by Mike Smith3.9k • written 13 months ago by pokharel.kisun0

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

ADD REPLYlink written 13 months ago by pokharel.kisun0
Answer: Ensembl sheep dataset in biomaRt
2
gravatar for Mike Smith
13 months ago by
Mike Smith3.9k
EMBL Heidelberg / de.NBI
Mike Smith3.9k wrote:

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.

ADD COMMENTlink written 13 months ago by Mike Smith3.9k
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