Entering edit mode
3.3 years ago
jeni ▴ 90
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.
Any reason why you don't think other preprocessing normalization options in minfi (SWAN or Functional normalization) could be even better?
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.