Hi, I'm trying to use Limma to analyse some nimblegen methylation data on MZ twins (imported through Ringo). The design is: Two colours microarray. One channel with a twin, the other channel with the other twin After 22 arrays we will observe the same pair (a twin for channel) but 10 years later: 1a 1b 2a 2b .... 1aAfter10 1bAfter10 2aAfter10 2bAfter10 ... I'd like to see: How similar are the MZ twins within each array 1a Vs 1b, etc How they change after 10 years (diverge? converge?) How each individual changes after 10 years (1a against 1aAfter10) The data are organized in regions of interest, therefore a variable number of probes exist for each region. It would be interesting comparing the methylations a whole, but also comparing the different region of interest. I find extremely difficult generating the design for this experiment and I'd be extremely grateful if you could help me. Best regards, Mario