HI, I ran
ComBat() for batch effect correction in my TCGA RNA-seq. consequently, I have two choices for batch effect correction: Parametric and nonparametric adjustment. So, I have down Parametric adjustment and resulted plot available in this link. Now, I need to know should I apply nonparametric adjustment
ComBat() on my data or not? I would like to know more about the interpretation of that plot.
I appreciate it if anybody shares his/her comment with me.