Differential Methylation in specific groups

Question

[rasii]

Hi all,

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.

Thanks,

Answer 1

[hongbo919]

What I guess is that your want to identify the group-specific DMRs from EPIC data. I suggest using the DMR identification software based on entropy such QDMR (for pre-defined regions) or SMART (for de novo identification of DMRs from BS-Seq data). As there are multiple samples in the same group, the DMC function of SMART should work for your project.