**290**wrote:

Hi,

I am analyzing methylation data, I have two files with beta values one for disease samples and another for control samples.

I would like to convert both disease and control beta values in to M values and calculate Fold change of disease/control using M values

I checked many articles and found that in some studies only beta values were used and delta B was calculated to assess DMR.

I tried both ways in the following example and found that different ways could give different assessemnt for a probe or position but i got different results

disease=.73

cont=.57

M_disease=1.434937

M_control=0.4066253

FC=M_disease/M_control=3.528893 which is differentially methylated in case threshold is 2 fold

delta B=.73-.57=.0.16 #NOT differentially methylated in case threshold=.2

Any one has an experience which has more robust output, using either delta B or FC for instance or using p-value of statistical tests as implemented in many R packages.

Any help is appreciated

**460**• written 3.7 years ago by Asma rabe •

**290**