Question

R biomaRt : listDatasets issue

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mamunbabu2001 • 0

@mamunbabu2001-16834

Last seen 5.7 years ago

Hi All,
I struggling to connect to ENSEMBL 93 using R biomaRt package.
listData set returns 68 datasets instead of 98 listed the example page and “hsapiens_gene_ensembl” is not included in the list.

> library("biomaRt")
> listMarts()

================

$               biomart               version
   1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 93
   2   ENSEMBL_MART_MOUSE      Mouse strains 93
   3     ENSEMBL_MART_SNP Ensembl Variation 93
   4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 93

> ensembl=useMart("ensembl")
> dim(listDatasets(ensembl))

> dim(listDatasets(ensembl))
[1] 68 3

> ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")

And when I try to connect using the dataset name I get the following error.

$ Error in checkDataset(dataset = dataset, mart = mart) :
The given dataset: hsapiens_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets() function.

Thanks in advance for help and suggestions.

Mamun

My R session details

==================

R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

locale:

[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base

other attached packages:
[1] BiocInstaller_1.28.0 biomaRt_2.34.2       annotate_1.56.2
[4] XML_3.98-1.13        AnnotationDbi_1.40.0 IRanges_2.12.0
[7] S4Vectors_0.16.0     Biobase_2.38.0       BiocGenerics_0.24.0

loaded via a namespace (and not attached):
[1] Rcpp_0.12.18    digest_0.6.15   bitops_1.0-6    xtable_1.8-2
[5] DBI_1.0.0       RSQLite_2.1.1   pillar_1.3.0    rlang_0.2.1
[9] blob_1.1.1      tools_3.4.1     bit64_0.9-7     RCurl_1.95-4.11
[13] bit_1.1-14      compiler_3.4.1 memoise_1.1.0   tibble_1.4.2

biomart • 815 views

ADD COMMENT • link updated 5.7 years ago by Mike Smith ★ 6.5k • written 5.7 years ago by mamunbabu2001 • 0

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Entering edit mode

This is a known issue on Ensembl's end. I had similar issues last week and was told that they resolved the issue. Have you tried a different ensembl host?

human <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl",host = "http://useast.ensembl.org/" )

Works for me

ADD REPLY • link 5.7 years ago stephen.williams ▴ 10

score 0 · Answer 1 · 2018-08-09

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 were 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.