I have methylation array data. I am using ChAMP package to process the data. What I noticed is when I run the function champ.norm(), the beta values comes different everytime. They are not too much different and generally the third decimmal place show bit up or down. It does not also change the overall output or interpretation. But heirarchical clustering at a later stage changes a bit.
Therefore, it will be good if I get same values everytime I run the function. More important questions is. Is it the package related issue or in general can happen with any R function? I tried to set.seed(1), but the values change again every time.
This might be new issue for me but some of you might have experienced it before. So I request you all to please guide me in this.