Bioequivalence and Bioavailability Forum

Hi Risherd,

I think this issue is related to the denominator of the F-test.

The sequence factor level is unique between subjects (not within) and therefore the sequence effect is often tested with the between-subject-MS in the denominator - this is what the bogus random statement in SAS effectuates. I think WinNonLin doesn't do it this way.

I have a feeling Bear does this as well. It can be rather easily implemented, although at the outset R will not by default do it this way but will spit out a 'normal' table where all fixed factors are tested with the residual MS in the denominator.

Try this:

1. Look at the anova table from WNL and add the sums of squares incl. the residual. If they add up to the null sums of sqaures, then it means that WNL does not test the Seq effect with the between-subject variability in the denominator for the F-test.
   
2. Try to remove the bogus statement from the SAS script and compare directly with WNL.

PS - to yjlee: For type III SS you can use drop1 in R, or you can work around manually by adding and removing factors in the lm specification. For Seq, the latter might be the best option since Subjects are uniquely split out on Seqs. A drop1 with Subj, Seq, Per, Trt as factors will for Seq just give flat zero (plusminus some machine/convergence precision) due to the design.