Question

minfi latest update for EPIC V2 chip

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e1271094 • 0

@5a72c261

Last seen 7 months ago

Singapore

Hi everyone,

May I ask what is the most updated EPIC V2 chip analysis using minfi package?

Is it still using the annotation provided by jokergoo?

install("jokergoo/IlluminaHumanMethylationEPICv2manifest")

install("jokergoo/IlluminaHumanMethylationEPICv2anno.20a1.hg38")

And would anyone be kind enough to share the latest pipeline to process EPIC V2 chip methylation data?

Thank you very much.

minfi minfiDataEPIC • 1.4k views

ADD COMMENT • link updated 2 days ago by macdonaldfrench7286566 • 0 • written 8 months ago by e1271094 • 0

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Did you happen to get it?

ADD REPLY • link 11 weeks ago Aurora • 0

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Yes, the most updated analysis for the EPIC V2 chip using the minfi package still involves using the annotations provided by jokergoo.

This post was last modified: 31-12-2024, 04:10 am by space waves

ADD REPLY • link 2 days ago macdonaldfrench7286566 • 0

score 2 · Answer 1 · 2024-05-07

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 1 day ago

United States

Zuguang Gu submitted both of those packages as part of the current release, and I submitted a PR for minfi so it will now distinguish the original EPIC from the V2 chip. I don't know if there is a consensus as to what one should do with the individual forward and reverse strand probes however.

ADD COMMENT • link 8 months ago James W. MacDonald 67k