Bioequivalence and Bioavailability Forum

❝ Here is the ANOVA of the first simulated study of our Scenario 1:

❝   Response: log(Y)

❝                          Df      Sum Sq      Mean Sq F value   Pr(>F)

❝   group                   1 0.171667589 0.1716675892 2.12908 0.151630 

❝   sequence                1 0.339810342 0.3398103421 4.21444 0.046057 *

❝   treatment               1 0.349206911 0.3492069106 4.33098 0.043277 *

❝   group:period            2 0.224598347 0.1122991734 1.39277 0.259120 

❝   group:sequence          1 0.053695040 0.0536950403 0.66594 0.418865 

❝   group:treatment         1 0.252244911 0.2522449107 3.12843 0.083870 .

❝   group:sequence:subject 44 5.173880238 0.1175881872 1.45837 0.107359 

❝   Residuals              44 3.547717653 0.0806299467       

❝   ---

❝   Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

From the table above if I am not mistaken I see that sequence effect was tested by using a Residuals (=MSE) as an error term. Shouldnt sequence effect be tested by using subject(sequence) or in this case subject(group*sequence) as the error term because it is a between subject factor?

I am wondering if group*treatment is also a between-subject factor and should therefore be tested by using subject(group*sequence) as the error term and not Residuals (similarly as sequence effect)?
Because based on this post and your reply (thanks!) sex, sequence, stage, group, site and also sex*treatment are between-subject factors and should therefore be tested by using subject(group*sequence) or subject(sequence) (if we dont have group in the model) as the error term. If sex*treatment is a between-subject factor, I assume group*treatment should also be?

❝ And then …

❝   p.GxT[sim] <- anova(model1)[["group:treatment", "Pr(>F)"]]

❝ … which is 0.083870. Did we screw up?

Probably not but based on my explanation above shouldnt then F value for group*treatment be 2.14516? So 0.2522449107 divided by 0.1175881872?

PS Isn't MS Residuals (=MSE) generally always pretty smaller than MS subject(sequence) or subject(sequence*group) in case of groups?