Łukasz Ręcławowicz, Thanks. I got this p-value. > test() [1] P-value: 0.00139 I still could not figure out how to plot 5000 permuted Qtot vs Itot. -- View this message in context: http://r.789695.n4.nabble.com/Please-help-me-about-Monte-Carlo-Permutation-tp3017131p3018399.html Sent from the R help mailing list archive at Nabble.com.