Question

News:Ensembl 103 has been released

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mchakiachvili ▴ 20

@mchakiachvili-24016

Last seen 2.8 years ago

United Kingdom

Dear all

The new Ensembl marts for release 103 are now live on www.ensembl.org. If you are using biomaRt, you can change your host to access our most recent data:

ensemblmart103 <- useEnsembl(biomart=“ensembl")

PS: if you want force one previous version you can use: ensembl_101 <- useEnsembl(biomart = "ensembl", version = 101)

On behalf of Ensembl Team.

biomaRt ensembldb Ensembl ensemblVEP Biomart • 1.6k views

ADD COMMENT • link 3.9 years ago • updated 3.7 years ago mchakiachvili ▴ 20

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I tried this (it works fine with ensembl version 99)

ensembl_102 = useEnsembl(biomart="ensembl", version=102)

ensembl_102 = useDataset("hsapiens_gene_ensembl", mart=ensembl_102)

getBM(attributes=c('ensembl_gene_id', 'ensembl_gene_id_version',

'ensembl_transcript_id', 'ensembl_transcript_id_version',

'external_gene_name'),

filters = c('ensembl_gene_id'),

values = lungSet1_filter1$ensgene,

mart = ensembl_102)

and I get:

NULL Error in .processResults(postRes, mart = mart, sep = sep, fullXmlQuery = fullXmlQuery, : The query to the BioMart webservice returned an invalid result. The number of columns in the result table does not equal the number of attributes in the query. Please report this on the support site at http://support.bioconductor.org

Is there something wrong with my code or am I being too impatient?

I've tried setting the address of the archived version 102 as host, but it doesn't work. listMarts for version 102 returns this:

listMarts(host="https://nov2020.archive.ensembl.org") biomart version 1 ENSEMBL_MART_ENSEMBL Ensembl Genes 103 2 ENSEMBL_MART_MOUSE Mouse strains 103 3 ENSEMBL_MART_SNP Ensembl Variation 103 4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 103

ADD REPLY • link 3.9 years ago dobby.goes.science • 0

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Hi there, sorry for the late reply, I failed to reproduce your error, I don't have the values specified in your example, of course. Can you confirm the issue is still present?

Thanks for your patience. Marc (on behalf of EnsEMBL production team)

ADD REPLY • link 3.7 years ago mchakiachvili ▴ 20