Hi, I am using the dba.plotPCA function in DiffBind to get a PCA plot. Could someone tell me how to use the statistic test to test the separation between two clusters? If possible, could I add the 95% CI ellipses in dba.plotPCA function? Thanks a lot for your help!

What will you testing? What statement do you wish to be 95% confident about?

I am trying to know whether the two clusters are separated enough. Visually they are, but I just want to add some stats power. If not easily achieve, I am thinking to mark the 95% CI ellipses and illustrate the degree of overlapping/separation.

~~That's just a repeat of what you already said. 95% CI on what, exactly? For example, in a t-test, the confidence interval is for the difference in mean between the two populations being tested. A PCA is a tool to reduce dimensionality - I don't think it tests any hypotheses to give you confidence intervals.~~I'm sorry - I did not understand your question well. Does this SO post help: https://stackoverflow.com/questions/13936051/adding-ellipses-to-a-principal-component-analysis-pca-plot

Thank you for your help.