Question

unable to access Annotationhub latest record

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s.malik • 0

@89fab1ac

Last seen 12 weeks 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 • 997 views

ADD COMMENT • link updated 8 months ago by Tim Peters ▴ 200 • written 9 months ago by s.malik • 0

score 1 · Answer 1 · 2024-04-02

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Tim Peters ▴ 200

@tim-peters-7579

Last seen 11 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

ADD COMMENT • link 9 months ago Tim Peters ▴ 200

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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

ADD REPLY • link 8 months ago Chris Beam • 0

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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

ADD REPLY • link 8 months ago Tim Peters ▴ 200

score 0 · Answer 2 · 2024-04-02

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 7 days 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.

ADD COMMENT • link 9 months ago James W. MacDonald 67k

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yeah, just thought if there is any other option.

ADD REPLY • link 9 months ago s.malik • 0

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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.

ADD REPLY • link 9 months ago James W. MacDonald 67k