<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Dear Mamun,<div class=""><br class=""></div><div class=""><p style="box-sizing: border-box; margin: 0px 0px 10px; font-variant-ligatures: normal; orphans: 2; widows: 2;" class="">There was an issue with the biomaRt package and ensembl release 91 which would lead to the error you were seeing. Please see <a rel="nofollow" href="https://support.bioconductor.org/p/104025/#104043" style="box-sizing: border-box;" class="">A: biomaRt: drerio_gene_ensembl dataset missing </a>or <a rel="nofollow" href="https://www.biostars.org/p/289654/#289861" style="box-sizing: border-box;" class="">https://www.biostars.org/p/289654/#289861</a> for more details.</p><div class="">Updating your biomaRt package will fix the issue, more information here: <a href="https://www.bioconductor.org/install/#update-bioconductor-packages" class="">https://www.bioconductor.org/install/#update-bioconductor-packages</a></div><div class=""><br class=""></div><div class="">Hope this helps,</div><div class="">Kind Regards,</div><div class="">Thomas</div><div class=""><div><blockquote type="cite" class=""><div class="">On 7 Aug 2018, at 15:58, rm8 <<a href="mailto:rm8@sanger.ac.uk" class="">rm8@sanger.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi All,<div class="">I struggling to connect to ENSEMBL 93 using R biomaRt package. </div><div class="">listData set returns 68 datasets instead of 98 listed the example page and “<b class="">hsapiens_gene_ensembl</b>” is not included in the list. </div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><div class="">> library("biomaRt")</div><div class="">> listMarts()</div><div class=""><br class=""></div><div class="">================</div><div class=""><br class=""></div><div class="">$ biomart version</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>1 ENSEMBL_MART_ENSEMBL Ensembl Genes 93</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>2 ENSEMBL_MART_MOUSE Mouse strains 93</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>3 ENSEMBL_MART_SNP Ensembl Variation 93</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 93</div><div class=""><br class=""></div><div class="">> ensembl=useMart("ensembl")</div><div class="">> dim(listDatasets(ensembl))</div><div class=""><br class=""></div><div class="">> dim(listDatasets(ensembl))</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>[1] <b class="">68</b> 3</div><div class=""> <span class="Apple-tab-span" style="white-space:pre"> </span></div></div><div class=""><br class=""></div><div class=""><div class="">> ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">And when I try to connect using the dataset name I get the following error. </div><div class=""><br class=""></div><div class="">$ <b class="">Error in checkDataset(dataset = dataset, mart = mart) : </b></div><div class=""><b class=""> The given dataset: hsapiens_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets() function.</b></div></div><div class=""><br class=""></div><div class=""> </div><div class="">Thanks in advance for help and suggestions. </div><div class=""><br class=""></div><div class="">Mamun</div></div>_______________________________________________<br class="">Dev mailing list <a href="mailto:Dev@ensembl.org" class="">Dev@ensembl.org</a><br class="">Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" class="">http://lists.ensembl.org/mailman/listinfo/dev</a><br class="">Ensembl Blog: <a href="http://www.ensembl.info/" class="">http://www.ensembl.info/</a><br class=""></div></blockquote></div><br class=""><div class="">
<div class=""><div class="" style="orphans: 2; widows: 2;">--</div><div class="" style="orphans: 2; widows: 2;">Thomas Maurel<br class="">Bioinformatician - Ensembl Production Team<br class="">European Bioinformatics Institute (EMBL-EBI)<br class="">European Molecular Biology Laboratory<br class="">Wellcome Trust Genome Campus<br class="">Hinxton<br class="">Cambridge CB10 1SD<br class="">United Kingdom</div></div>
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