Also, I get these:

Warning messages:

1: 'memory.size()' is Windows-specific

2: 'memory.size()' is Windows-specific

3: 'memory.size()' is Windows-specific

4: 'memory.size()' is Windows-specific

5: 'memory.size()' is Windows-specific

6: 'memory.size()' is Windows-specific

7: 'memory.size()' is Windows-specific

8: 'memory.size()' is Windows-specific

9: 'memory.size()' is Windows-specific

10: 'memory.size()' is Windows-specific

11: 'memory.size()' is Windows-specific

12: 'memory.size()' is Windows-specific

13: 'memory.size()' is Windows-specific

14: 'memory.size()' is Windows-specific

15: 'memory.size()' is Windows-specific

16: 'memory.size()' is Windows-specific

17: 'memory.size()' is Windows-specific

18: 'memory.size()' is Windows-specific

19: 'memory.size()' is Windows-specific

20: In GAPIT.Main(Y = ic_Y, GD = DP$GD[, -1], GM = DP$GM, ... :

The upper bound of groups is too high. It was set to the size of kinship!

21: In GAPIT.Main(Y = ic_Y, GD = DP$GD[, -1], GM = DP$GM, ... :

The lower bound of groups is too high. It was set to the size of kinship!

22: 'memory.size()' is Windows-specific

23: 'memory.size()' is Windows-specific

24: 'memory.size()' is Windows-specific

25: 'memory.size()' is Windows-specific

26: 'memory.size()' is Windows-specific

27: 'memory.size()' is Windows-specific

28: 'memory.size()' is Windows-specific

29: 'memory.size()' is Windows-specific

30: 'memory.size()' is Windows-specific

31: 'memory.size()' is Windows-specific

32: 'memory.size()' is Windows-specific

33: 'memory.size()' is Windows-specific

34: 'memory.size()' is Windows-specific

35: 'memory.size()' is Windows-specific

36: 'memory.size()' is Windows-specific

37: 'memory.size()' is Windows-specific

38: 'memory.size()' is Windows-specific

39: 'memory.size()' is Windows-specific

40: 'memory.size()' is Windows-specific

41: 'memory.size()' is Windows-specific

42: 'memory.size()' is Windows-specific

43: 'memory.size()' is Windows-specific

44: 'memory.size()' is Windows-specific

45: In rm(dfs) : object 'dfs' not found

46: In rm(stats) : object 'stats' not found

47: In rm(effect.est) : object 'effect.est' not found

48: In rm(ps) : object 'ps' not found

49: In rm(nobs) : object 'nobs' not found

50: In rm(maf) : object 'maf' not found

Hi, Dr Sanchez, maybe you can try the "GLM" model.

Sometimes, the CMLM model is not suite for your data.

For instance,

If the observered point set showed lower than the expected, it means that there might be a overcorrection by K-matrix or Q-matrix.

At the moment, you should change the model according to the QQ plot, namely remove the parameter of K or Q.

I hope I can help you.

So you might have type 2 errors, ie. failing to reject the null hypothesis when it's not true. So you could increase the significance level, but usually it is increased to 0.1, so that won't help. Or you can increase the sample size of the test to increase its power. Or try a different model as mentioned by Ming Yang :)