[BioC] mr.edgeR tests in MEDIPS package

[Matthias Lienhard]

Hi Kelly,

the CSet is used for CpG dependent normalization ("rms" and "prob") 
only, and does not effect the differential coverage test results (logFC, 
pvalue ...) calculated by edgeR. To avoid confusion, you could set MeDIP 
to FALSE, then the CpG normalized values are not calculated.

Best, Matthias

On 05/16/14 18:17, Vining, Kelly wrote:
> Hello,
> I am using the MEDIPS package to find differentially-methylated regions among three developmental stages, following the vignette, and have a question about how
> differential coverage us calculated.
>
> The differential coverage step, from the vignette:
>> mr.edgeR = MEDIPS.meth(MSet1 = DE_MeDIP, MSet2 = hESCs_MeDIP,
> + CSet = CS, ISet1 = DE_Input, ISet2 = hESCs_Input, p.adj = "bonferroni",
> + diff.method = "edgeR", prob.method = "poisson", MeDIP = T,
> + CNV = F, type = "rpkm", minRowSum = 1)
>
> Here, CSet is "coupling set", which is used for CpG-dependent normalization of the MEDIPS SETs. For my own run, I have designated a CSet, and have an Input comparator. What I am unsure about is whether, at this step, cytosine context is being taken into account. It doesn't look like it matters whether cytosines are in CG context or not, but since MEDIPS appears to have been designed specifically for human cancer studies, and my MeDIP samples are from plants, where cytosines in all contexts can be differentially methylated, I want to make sure that I'm not losing data at this step in the analysis.
>
> Thanks for help,
> --Kelly V.
>
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