Question: Question about MEDIPS
3
gravatar for hxlei613
5.4 years ago by
hxlei61390
Bangladesh
hxlei61390 wrote:

Hello,everyone!

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 identifie 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 dont understand why the same regions with the same rms 1  in the two datasets can be selected out. I dont think the same rms also means significant differential coverage.

I am totally new in the field of bioinformatics . Can any body help me ? Thank you very much !

 

methylation dmr medips R • 1.8k views
ADD COMMENTlink modified 5.2 years ago by Biostar ♦♦ 20 • written 5.4 years ago by hxlei61390
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