Hi, I have a question of using sample Data.
I want to try some experiments of using classification method for cancer classification using DNA methylation values.
I will use methylation beta value of TCGA solid tumor for cancer data.
A question I have is that I want to use normal sample data to compare the methylation value of specific CpG sites.
Here, I am confused in whether I should use healthy control sample data, or whether I can use normal tissue sample of patients who have cancer.
For example, I have methylation beta value of cpg00001 in solid tumor tissue of breast cancer patient. And to compare this, I have cpg00001 value in solid tissue normal of same breast cancer patient.
Is it possible to use like this?