I have 18 samples organized by sample_type (2 types) x time_point (3 time points)
Is it possible to perform a differential methylation analysis with rnb.execute.computeDiffMeth to compute
diff_meth for type1_vs_type2 showing the dynamics across the time points (similarly to analysis formula in DESeq2 for RNA-seq: ~ sample_type + time_point).
I tried to set up the table and the pairwise flag, but I got results "time point1 vs everything else", instead of time1 vs time2, time2 vs time3.
What would you your best practice for such an analysis with RbBeads?
Hello epigen team!
Thanks for the useful package!
I have 18 samples organized by sample_type (2 types) x time_point (3 time points)
Is it possible to perform a differential methylation analysis with rnb.execute.computeDiffMeth to compute diff_meth for type1_vs_type2 showing the dynamics across the time points (similarly to analysis formula in DESeq2 for RNA-seq: ~ sample_type + time_point).
I tried to set up the table and the pairwise flag, but I got results "time point1 vs everything else", instead of time1 vs time2, time2 vs time3.
What would you your best practice for such an analysis with RbBeads?
Sergey