SVA package for RRBS - bisulfite methylation data
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GFM ▴ 20
@gfm-8326
Last seen 9 months ago
European Union

Hello,

I have data of methylation percentages of tiles (from rrbs bisulfite experiment).

Is it possible to use the SVA package for batch effect correction? If so, what should the input be - the actual percentages?

Thanks

rrbs batch effect methylation sva • 1.1k views
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Hi,

Did you get any further with this? I've just hit the same problem, and am struggling to find specific examples of correcting batch effects in RRBS data.

Thank you,

David

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Jeff Leek ▴ 610
@jeff-leek-5015
Last seen 7 months ago
United States

Hi Ray

I have heard of folks using SVA on this type of data, but they usually do it on something like the logit transformed percentage scale. I haven't actually tried it myself though so I'm not totally sure how it will work. The assumptions behind the sva algorithm require an approximately symmetric distribution that isn't bounded - percentages may not work great particularly for very low levels or high levels. 

 

Best

 

Jeff

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Thanks a lot for the answer!

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