So I finally got the Day 10 files processed through methpipe and have been trying to get RADMeth to work all day. After combining the different samples in to a single file and building the design matrix, it keeps giving me a sample out of order/not matching the design matrix error. I’m not sure what’s going on, but I’ve applied to join the methpipe Google group, and hopefully someone there can help me.

notebook entry: http://rpubs.com/seanb80/261272