Question

how to run old scripts using corresponding biomaRt versions from archives

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Didi ▴ 10

@didi-10905

Last seen 2.1 years ago

Spain

Hi,

Is there a way I can check the archive versions of bioamRt and then use one them to run. I have an old scripts from 2016, 2017 and 2018 and I want to rerun them with their corresponding version of biomaRt.

Thanks a lot.

D.

biomaRt Bioconductor • 831 views

ADD COMMENT • link updated 4.8 years ago by Mike Smith ★ 6.5k • written 4.8 years ago by Didi ▴ 10

score 1 · Answer 1 · 2019-07-09

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Mike Smith ★ 6.5k

@mike-smith

Last seen 2 hours ago

EMBL Heidelberg

You don't need to use an old version of biomaRt, Ensembl provide archive versions of their site that you can use. You can list the available archives with listEnsemblArchives() and choose one by providing the version argument to useEnsembl()

ADD COMMENT • link 4.8 years ago Mike Smith ★ 6.5k

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Thanks a lot for your answer. I have this script from 2016.

 library(biomaRt)
    mart = useEnsembl(biomart="plants_mart", host="plants.ensembl.org", dataset = "osativa_eg_gene")
    bm <- useMart(host = "plants.ensembl.org", biomart="plants_mart", dataset = "osativa_eg_gene")

I couldn't manage to make it work adding the version argument to useEnsembl(). I added version="84" and got this error Error: Specified Ensembl version is not available. Use listEnsemblArchives() to view available versions.

ADD REPLY • link 4.8 years ago Didi ▴ 10

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I think I need to spend some time clarifying / updating the useEnsembl() function because it's primarily focused on the main Ensembl site, rather than EnsemblGenomes - that's understandably not clear from the function name!

The only archive that I know of for Ensembl Plants is from October 2017 (http://oct2017-plants.ensembl.org/). I'm not sure there's any way to access the annotation that was present in 2016 if Ensembl are not making it available. Using and older version of biomaRt will still access the most recent data.

ADD REPLY • link 4.8 years ago Mike Smith ★ 6.5k