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clarisbaby
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@clarisbaby-14317
Last seen 6.6 years ago
Hey everyone, I am trying to use C. elegans dataset available from biomaRt for annotation purpose. The commands I use runs at a given point of time and shows no error while the same command give error when run again. I have tried to run different variations for the same command, but each one has the same issue. Please guide me through, as I am trying to incorporate this command in one of the RNA-seq analysis package i am developing... the following is the codes i have used and the error messages received 1. > m <- useMart(biomart="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", path="/biomart/martservice", dataset="celegans_gene_ensembl") Error in checkDataset(dataset = dataset, mart = mart) : The given dataset: celegans_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets() function. > m <- useMart(biomart="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", path="/biomart/martservice", dataset="celegans_gene_ensembl") Error in checkDataset(dataset = dataset, mart = mart) : The given dataset: celegans_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets() function. > m <- useMart(biomart="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", path="/biomart/martservice", dataset="celegans_gene_ensembl") 2. > m <- biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "celegans_gene_ensembl", host = 'ensembl.org') Error in checkDataset(dataset = dataset, mart = mart) : The given dataset: celegans_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets() function. > m <- biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "celegans_gene_ensembl", host = 'ensembl.org')
3. > m <- useMart("ensembl",dataset=("celegans_gene_ensembl")) Error in checkDataset(dataset = dataset, mart = mart) : The given dataset: celegans_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets() function. > m <- useMart("ensembl",dataset=("celegans_gene_ensembl")) Error in checkDataset(dataset = dataset, mart = mart) : The given dataset: celegans_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets() function. > m <- useMart("ensembl",dataset=("celegans_gene_ensembl")) > sessionInfo()
R version 3.4.0 (2017-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.2 LTS Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.6.0 LAPACK: /usr/lib/lapack/liblapack.so.3.6.0 locale: [1] LC_CTYPE=en_IN.UTF-8 LC_NUMERIC=C LC_TIME=en_IN.UTF-8 LC_COLLATE=en_IN.UTF-8 [5] LC_MONETARY=en_IN.UTF-8 LC_MESSAGES=en_IN.UTF-8 LC_PAPER=en_IN.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] RNAseq_0.1.0 biomaRt_2.32.1 knitr_1.17 Rqc_1.10.2 [5] ggplot2_2.2.1 GenomicFeatures_1.28.5 AnnotationDbi_1.38.2 systemPipeR_1.10.2 [9] ShortRead_1.34.1 GenomicAlignments_1.12.2 SummarizedExperiment_1.6.5 DelayedArray_0.2.7 [13] matrixStats_0.52.2 Biobase_2.36.2 BiocParallel_1.10.1 Rsamtools_1.28.0 [17] Biostrings_2.44.2 XVector_0.16.0 GenomicRanges_1.28.6 GenomeInfoDb_1.12.2 [21] IRanges_2.10.4 S4Vectors_0.14.6 BiocGenerics_0.22.0 loaded via a namespace (and not attached): [1] backports_1.1.1 GOstats_2.42.0 Hmisc_4.0-3 [4] AnnotationHub_2.8.2 LSD_3.0 plyr_1.8.4 [7] lazyeval_0.2.0 GSEABase_1.38.2 splines_3.4.0 [10] BatchJobs_1.6 easyRNASeq_2.12.1 digest_0.6.12 [13] BiocInstaller_1.26.1 ensembldb_2.0.4 htmltools_0.3.6 [16] GO.db_3.4.1 gdata_2.18.0 magrittr_1.5 [19] checkmate_1.8.4 memoise_1.1.0 BBmisc_1.11 [22] BSgenome_1.44.2 cluster_2.0.6 DEXSeq_1.22.0 [25] limma_3.32.7 annotate_1.54.0 fail_1.3 [28] colorspace_1.3-2 blob_1.1.0 RCurl_1.95-4.8 [31] graph_1.54.0 roxygen2_6.0.1 genefilter_1.58.1 [34] ape_4.1 brew_1.0-6 survival_2.41-3 [37] sendmailR_1.2-1 VariantAnnotation_1.22.3 gtable_0.2.0 [40] zlibbioc_1.22.0 scales_0.5.0 DESeq_1.28.0 [43] vsn_3.44.0 pheatmap_1.0.8 DBI_0.7 [46] edgeR_3.18.1 Rcpp_0.12.13 xtable_1.8-2 [49] htmlTable_1.9 foreign_0.8-69 bit_1.1-12 [52] preprocessCore_1.38.1 Formula_1.2-2 intervals_0.15.1 [55] AnnotationForge_1.18.2 htmlwidgets_0.9 httr_1.3.1 [58] gplots_3.0.1 RColorBrewer_1.1-2 acepack_1.4.1 [61] reshape_0.8.7 pkgconfig_2.0.1 XML_3.98-1.9 [64] Gviz_1.20.0 nnet_7.3-12 locfit_1.5-9.1 [67] rlang_0.1.2 reshape2_1.4.2 munsell_0.4.3 [70] tools_3.4.0 qrqc_1.30.0 RSQLite_2.0 [73] devtools_1.13.3 evaluate_0.10.1 stringr_1.2.0 [76] yaml_2.1.14 bit64_0.9-7 caTools_1.17.1 [79] AnnotationFilter_1.0.0 ASpli_1.2.3 nlme_3.1-131 [82] RBGL_1.52.0 mime_0.5 xml2_1.1.1 [85] genomeIntervals_1.32.0 BiocStyle_2.4.1 compiler_3.4.0 [88] curl_2.8.1 interactiveDisplayBase_1.14.0 affyio_1.46.0 [91] tibble_1.3.4 statmod_1.4.30 geneplotter_1.54.0 [94] stringi_1.1.5 GenomicFiles_1.12.0 lattice_0.20-35 [97] ProtGenerics_1.8.0 Matrix_1.2-11 commonmark_1.4 [100] markdown_0.8 data.table_1.10.4 bitops_1.0-6 [103] httpuv_1.3.5 rtracklayer_1.36.5 affy_1.54.0 [106] R6_2.2.2 latticeExtra_0.6-28 hwriter_1.3.2 [109] KernSmooth_2.23-15 gridExtra_2.3 dichromat_2.0-0 [112] gtools_3.5.0 DESeq2_1.16.1 Category_2.42.1 [115] rprojroot_1.2 rjson_0.2.15 withr_2.0.0 [118] GenomeInfoDbData_0.99.0 grid_3.4.0 rpart_4.1-11 [121] rmarkdown_1.6 biovizBase_1.24.0 shiny_1.0.5 [124] base64enc_0.1-3
It would be very kind if anyone can suggest me where I am going wrong and how to use this command
Thanks in advance.
Thanku so much @Mike Smith. The above stated command worked just fine and some of my packages do seem to be out-of-date, I will surely try and update them. Thanks for the suggestion too.