Combining analysis of EPICv1 and EPICv2 using SeSAMe package

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archibold.mposhi • 0

@0beeedc8

Last seen 16 months ago

Luxembourg

Hello,

I would like to know if anyone has ever tried to analyse both EPICv1 and EPICv2 arrays at the same time. I am working on a project where we have used both V1 and V2. Our main challenge now is combining the data we obtained from the 2 different EPIC versions. We are using the SeSAMe package for our analysis. Anyone with information on how to get around this please assist. Many thanks in advance!

sesameData EPICv2 EPICv1 • 2.3k views

ADD COMMENT • link updated 4 months ago by Mancy • 0 • written 16 months ago by archibold.mposhi • 0

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Hi, would you advise, how did you manage this case?

ADD REPLY • link 12 months ago rania.alanany • 0

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Just FYI, the new mLiftOver feature in sesame is designed to address this issue. https://academic.oup.com/bioinformatics/article/40/7/btae423/7705981 Hope it helps.

ADD REPLY • link 12 months ago zhouwanding ▴ 20

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@block blast Thank you for giving us that experience. We hope you will share more with us!

ADD REPLY • link 4 months ago Mancy • 0

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Have you tried using only the shared probes between the two arrays for downstream analysis? I believe SeSAMe supports probe filtering block blast, which could help harmonize the datasets.

ADD REPLY • link 4 months ago morton • 0

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