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