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Minfi preprocessNoob vs preprocessQuantile normalization for Illumina EPIC array

Hi,

I would be very grateful if someone could explain me which method is better to use for differencial methylation analysis of 2 groups of samples from the same tissue (the difference is that one group respond and the other don't to a treatment). Would it be better to apply Noob or Quantile normalization? and what is the reason for that?

Thanks in advance.

r minfi bioconductor
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updated by zx8754 zx8754 • written by jeni • jeni

Any reason why you don't think other preprocessing normalization options in minfi (SWAN or Functional normalization) could be even better?

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written by igor igor

Thanks for your response. Actually I am not sure about what to use; but what I undestood from what I read is that Noob and Quantile are the more appropiate methods for closer groups, while the others are better for globally different groups.

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written by jeni • jeni

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