Query Regarding Outlier Removal in RRBS Data Analysis Using MethylKit

Question

[Srinka]

Is it necessary to remove outliers in RRBS data analysis using MethylKit, and if so, what is the recommended method for outlier removal?

I've employed the clusterSamples and PCASamples functions to detect outliers in my methylbase object. However, I'm seeking advice on the subsequent steps and best practices for effectively removing these outliers from my dataset.

Thank you in advance.