Question: SVA package for RRBS - bisulfite methylation data
0
gravatar for GFM
4.0 years ago by
GFM20
European Union
GFM20 wrote:

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

ADD COMMENTlink modified 2.8 years ago by dashbrook10 • written 4.0 years ago by GFM20

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

ADD REPLYlink written 2.8 years ago by dashbrook10
Answer: SVA package for RRBS - bisulfite methylation data
0
gravatar for Jeff Leek
4.0 years ago by
Jeff Leek560
United States
Jeff Leek560 wrote:

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

ADD COMMENTlink written 4.0 years ago by Jeff Leek560

Thanks a lot for the answer!

ADD REPLYlink written 4.0 years ago by GFM20
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