I'm really new to all this methylation stuff so was wondering if you guys can help me. I have some patient samples that I have analysed methylation with the Illumina methylation EPIC microarray. I am using RnBeads to analyse the data which has worked awesome. I'm stuck at the differential methylation part because I need to compare only specific groups.
In my data set I have 3 sample groups - Baseline, Treat 1 and Treat 2 The comparison I would like to do are : 1- Baseline vs Treat 1; 2- Basseline vs Treat 2 and Treat 1 vs treat 2
How can I write the code so that I can analyse the diff in methylation for these comparisons individually? And after each comparison I would like get the table so I can do pathway analysis.