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  • $\begingroup$ Is it possible that you did not convert the predictors to factor variables before computing the results? It might be possible that Variable I with levels 1, 2, ... is seen as numerical, which would lead to erroneous results with the first two approaches. $\endgroup$ Commented Jan 24, 2023 at 14:34
  • $\begingroup$ @David I did convert the predictors to factor variables (I just checked). So that's not it... $\endgroup$ Commented Jan 24, 2023 at 14:53
  • $\begingroup$ I don't use rstatix, but a quick look at the manual suggests that you need to specify a random-effect term similar to that you used in Method 1. See the example in the anova_test help section on the "formula" argument for "Within-SsANOVA(repeatedmeasuresANOVA)." $\endgroup$ Commented Jan 24, 2023 at 14:55
  • $\begingroup$ @EdM it doesn't seem to be working. When I use the formula approach I get: Error in Error(ID) : could not find function "Error". The manual is inconsistent with the use of the Error term in the formular it sometimes uses Error() and sometimes error(), I tried both and none of these worked. $\endgroup$ Commented Jan 24, 2023 at 15:03