Question: Methylation Data Interpretation and Dychotomization
gravatar for luisa
23 months ago by
luisa10 wrote:

Hi! I am working with methylation data from the TCGA Database. I chose the file with the mean signal values among each gene... The data presented is beta-values, which range from 0 to 1, where 0 means the gene is not methylated and 1 that the gene is totally methylated, however there are values in between and I am trying to dycotomize my data into methylated/non-methylated... What is the best way to set a threshold to define my two groups?

Thanks in advance!

methylation tcga • 744 views
ADD COMMENTlink modified 23 months ago by suleymanvural40 • written 23 months ago by luisa10
gravatar for suleymanvural
23 months ago by
United States
suleymanvural40 wrote:

Not a simple task. See the post here A: Interpreting Fractional Methylation Data

ADD COMMENTlink written 23 months ago by suleymanvural40

Just to add: I recently set Beta=0.6 as a 'hard' threshold and our work has just been accepted for publication in OncoTarget.

There is no real answer, though. It's like fold change differences in expression studies.

ADD REPLYlink written 23 months ago by Kevin Blighe54k

I actually think that is the easiest way... I have also seen other papers that take that approach. However, as you say I have already come across various methods to do this... I think I will look at my data and set an empirical threshold... Thank you both!

ADD REPLYlink written 23 months ago by luisa10
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