I have been using minfi for doing differential methylation analysis, and
now I have some studies with paired samples.

Do minfi have a way of defining a paired analysis both in the categorical
and continuous dmpFinder analysis?

Under the hood minfi uses limma, so one possibility is to use the code of
dmpFinder and modify to do paired contrasts (well first I would need to
refresh how to do this contrast in limma).

I have a classical followup design study:

treatment_A-basal
treatment_A-xyears
treatmen_B-basal
treatment_B-xyears

Where basal and xyears for each treatment have the same samples

If minfi does not have the ability to do the paired analysis, could I have
some pointers how to do it with limma. Probably I am wrong bu,t by the
nature of the chip design, should I follow the limma examples in the
vignette for one color array?

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