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Old 04-26-2017, 07:56 AM   #1
GB1
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Location: London

Join Date: Apr 2017
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Default MEDIPS DMR identification

Hi

I am trying to analyse some MeDIP-seq data using MEDIPS. I would like to perform differential methylation analysis between controls (C57_data) and a mutant sample (gtgt_data). I have attempted to do this using:

results_C57_vs_gtgt=MEDIPS.meth(MSet1 = C57_data, MSet2 = gtgt_data,
+ CSet = CS, p.adj = "bonferroni", diff.method = "edgeR", MeDIP = T, CNV = F)

However, I get the following error message:

Error in MEDIPS.calibrationCurve(MSet = MSet1[[i]], CSet = CSet, input = F) :
The dependency of coverage signals on sequence pattern (e.g. CpG) densities is different than expected. No linear model can be build, please check the calibration plot by providing the MSet object at ISet.

I have attempted to plot the calibration plot, but get a similar error.

I understand that the failure to build a proper linear model may be because there is not a linear dependency of CpG density and MeDIP-seq signal in my data.

I do not have input data for either control or mutant sample.

Is there a way to perform the differential methylation analysis on my data using MEDIPS despite this?

Any help would be much appreciated

Many thanks

G
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