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