Question: how to run old scripts using corresponding biomaRt versions from archives
0
gravatar for Didi
4 months ago by
Didi10
Didi10 wrote:

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 • 133 views
ADD COMMENTlink modified 4 months ago by Mike Smith4.0k • written 4 months ago by Didi10
Answer: how to run old scripts using corresponding biomaRt versions from archives
1
gravatar for Mike Smith
4 months ago by
Mike Smith4.0k
EMBL Heidelberg / de.NBI
Mike Smith4.0k wrote:

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 COMMENTlink written 4 months ago by Mike Smith4.0k

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 REPLYlink modified 4 months ago • written 4 months ago by Didi10

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 REPLYlink written 4 months ago by Mike Smith4.0k
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