batch effect in EPIC array data

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Jitendra ▴ 10

@nabiyogesh-11718

Last seen 5 months ago

United Kingdom

Hi all,

Could anyone please suggest best way how to find batch effect in EPIC array methylation data and then how to remove it.

Many thanks,

statistics Epigenetics R • 1.5k views

ADD COMMENT • link updated 21 months ago by Lluís Revilla Sancho ▴ 760 • written 21 months ago by Jitendra ▴ 10

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Do you have some data or this is purely theoretical? I created a package to help detect it before it is sequenced and avoid having problems when sequencing in multiple batches: experDesign . If you want to remove it probably limma::removeBatchEffect works, but there might be more specific methods.

ADD REPLY • link 21 months ago Lluís Revilla Sancho ▴ 760

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I do have epigenetic data. In one of the paper below approached was used but not sure whether to go for this or there are some other way to do it; I am also not sure what R script they used here; not able find to detail description about it.

The models were fitted with the lme4 R package102. Strong associations were observed between the first four PCs and slide position and sample plate (Supplementary Fig. 1f, g). M values were thus corrected for these two batch effects using the ComBat function, from the sva R package-

https://www.nature.com/articles/s41467-022-33511-6#Sec12

ADD REPLY • link 21 months ago Jitendra ▴ 10

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Well it tells you they used sva::combat. You can contact the authors and ask for the exact script they used.

ADD REPLY • link 21 months ago Lluís Revilla Sancho ▴ 760

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