unable to access Annotationhub latest record
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s.malik • 0
@89fab1ac
Last seen 16 days ago
Pakistan

Hi, I am trying to access a recently added annotation of EPICv2 DNA methylation array from AnnotationHub using the code below but cannot retrieve it. I found this modified manifest useful from recent paper; https://bioconductor.org/packages/devel/data/annotation/vignettes/EPICv2manifest/inst/doc/EPICv2manifest.html

> ah <- AnnotationHub()
> EPICv2manifest <- ah[["AH116484"]]
Error: AH116484 added after current Hub snapshot date.
  added: 2024-02-09
  snapshot date: 2023-10-23
  To access this resource update your version of Bioconductor

R 4.3.3, Bioconductor 3.18, BiocManager 1.30.22, AnnotationHub 3.10.0

Do I need to update Bioconductor to development version? that needs R to be 4.4 and I don't want that, any quick fix plz? Thanks

DNAMethylation AnnotationHub EPICv2manifest annotation • 295 views
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@james-w-macdonald-5106
Last seen 15 hours ago
United States

You are pointing to a devel package, but are using the release version of R/Bioc. To use the package you need R-devel and Bioc-devel, or to wait for the upcoming release.

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yeah, just thought if there is any other option.

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No, everything in Bioconductor is tightly linked to the versions of R and Bioconductor to ensure operability. So devel packages (in spring at least) require R-devel.

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Tim Peters ▴ 170
@tim-peters-7579
Last seen 3 days ago
Australia

Hello,

To access the manifest, you can download it in CSV format as Additional file 4 here: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-024-10027-5#Sec31. Click on "Additional File 4" (it's quite large, over 1GB).

Cheers, Tim

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Dear Tim,

Is "Additional file 4" in https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-024-10027-5#Sec31 the same as the "EPIC-8v2-0_A2.csv" manifest file available at Illumina's webpage?

Thank you, Chris

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Hi Chris,

It is based off that manifest file but contains 31 additional columns describing some of the results in the paper. All cg and ch probes are present (rs, nv and control probes have been removed).

Cheers, Tim

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