DNA methylation preprocessing
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5 months ago
SYOSY • 0

Hi,

I studying about DNA methylation analysis.

In R, minfi package provide many normalization methods. (for example, SWAN, Funnorm etc..)

but i don't know what is difference of these..

Funnorm methylation Raw SWAN DNA • 459 views
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Have you read the documentation, vignette, and associated papers?

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Yes..

but i don't understand it well..

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4 months ago
Marc ▴ 10

I happen to be writing a paper that compares preprocessing in minfi, sesame, and methylsuite so I can offer AN answer. However, know that different researches prefer different ways to process data and there is no one universally accepted "right" way.

enter image description here

Minfi has at least 5 ways to clean up the raw probe intensities. Of these, methylprep (of which I am the maintainer) and sesame (another R package we benchmark against) opt for pOOBAH, NOOB, and a nonlinear dye bias correction based on quantile normalization. Minfi doesn't offer 2 of these but does have a preprocessNOOB step. I would use that over SWAN and its quantile normalization and the other options.

The end result is that you get cleaned data that is more comparable across batches and between studies. Differences in background fluorescence are minimized and the beta values you calculate are shifted closer to 0 and 1, better matching what we'd expect.

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