I've got two MeDIP-Seq datasets (one is normal and another is treated with medicine or something, from the same patient). The point is that I want to identify differentially methylated regions (DMR) between these two datasets.
I made the alignment step using BWA, then I'm trying MEDIPS. I'm following the tutorial http://www.bioconductor.org/packages/release/bioc/vignettes/MEDIPS/inst/doc/MEDIPS.pdf.
The two datasets are MP1.bam and MP2.bam. I followed every step until chapter 4.3 because I find that the result I got is strange. I don't have INPUT SET. I specify MP1 as the coupling set. In chapter 4.2, I specify MP1 as MSet1, MP2 as MSet2. The function is as following:
> mr = MEDIPS.meth(MSet1 = MP1, MSet2 = MP2, CSet = CS, p.adj = "bonferroni", diff.method = "edgeR", MeDIP = T, CNV = F, minRowSum = 10)
After that is chapter 4.3 "Differential coverage: selecting significant windows". I think in this step, the windows selected out can show significant differential coverage. The function is :
> diff = MEDIPS.selectSig(results = mr, p.value = 0.01, adj = T, ratio = NULL, bg.counts = NULL, CNV = F)
However, I find something strange in the result table. I don't understand why the same regions with the same rms 1 in the two datasets can be selected out. I don't think the same rms also means significant differential coverage.
I am totally new in the field of bioinformatics. Can anybody help me? Thank you very much!