I am a Biologist and have very less exposure to coding. My problem is, I have 300 samples beta matrix file of LUSC, which I have downloaded from TCGA. I have to run a Differential methylation Analysis on this data. I tried my best to work with ChAMP R package but I couldn't get it working. Currently, I have only beta matrix file and I don't have idat file as well.
Can you guys please let me know how to run the DMR analysis using ChAMP on beta-Matrix file? It would be really great if you can share codes.
Sorry for bothering, but I would be really happy if I can successfully run DMR on my matrix file.
Thanks in Advance.