biomaRt issue
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Fariz • 0
@c49fa6f2
Last seen 25 days ago
United States

Hi, I am trying to access the ensemble database but keep getting this error. Using bioconductor version 3.18(latest) and R version 4.3.1. The code here is to create a CNV object for recognizing tumor cells.


for (s in samples) {
  # Create inferCNV object and save it
  infercnv_obj <- createInferCNVObject_call(seurat_obj=seurat_obj, s=s)
}
Error: Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
http://jul2018.archive.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
biomaRt • 142 views
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Entering edit mode
Mike Smith ★ 6.4k
@mike-smith
Last seen 22 hours ago
EMBL Heidelberg

Did you try the URL in the error message? It redirects to a list of the Ensemble archives, and jul2018 doesn't appear in that list.

Ensemble has a 5 year lifetime for most of the archive sites, so the one from July 2018 has been decommissioned.

If createInferCNVObject_call is your function you'll need to update it. If it's from a package then you should contact the package maintainer.

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