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Which pipeline of DNA methylation analysis did you follow ?
sorry I don't know about pipeline. What do you mean by pipeline? i am using TCGA datasets
Which bioinformatic tool or packages are you using to perform your analysis ? Did you follow a specific tutorial ?
I am using TCGA datasets and R studio and Python as programming language .
You can follow some R tutorials that will help you to conduct a differential analysis, depending on the type of data you are analyzing :