I have a problem interpreting the output of the mixed model procedure in SPSS. I found a couple of threads dealing with similar problems, but none helped me solve it. I have a 2x2 repeated measures crossover design with two fixed factors (medication (A/B) and genotype (A/B)) and a random factor (timepoint (1/2)).

As I understand it, the output for the fixed effects is the general influence of the factors over all subgroups and the parameter estimates test the differences between levels. As I only have two levels for all my factors of interest the output should provide information about the difference between all levels from one that is used as 'baseline'.

This is the output:

Fixed effects Typ IIIa
source      df  df      F       p
Const       1   2,798   1753    0,000
gen*med     1   30,945  0,988   0,328
genotype    1   31,329  4,564   0,041
medication  1   30,953  12,886  0,001
a. Dependent variable: RT.

Parameter estimates
Parameter           est             sd      df      t       p       conf. int. 95 %
constant            385,695463  10,256203   4,450   37,606  0,000   358,320557  413,070370
[med=B] * [gen=A]   -6,220872   8,462102    40,021  -0,735  0,467   -23,323140  10,881395
[med=A] * [gen=A]   -19,875937  8,460116    39,989  -2,349  0,024   -36,974613  -2,777261
[med=B] * [gen=B]   7,742406    4,340784    30,949  1,784   0,084   -1,111266   16,596079
[med=A] * [gen=B]   0b  0   .   .   .   .   .
[gen=A] 0b  0   .   .   .   .   .
[gen=B] 0b  0   .   .   .   .   .
[med=B] 0b  0   .   .   .   .   .
[med=A] 0b  0   .   .   .   .   .

The questions are: is it correct to interpret this output as that there is a difference between medication(A) in genotype(A) compared to medication(A) in genotype(B)? If that is the case then I do not understand how to compare the effect of medication within genotype(A). Am I doing something wrong? I assume this output is correct for multiple comparisons. Is that correct?

The code is:

MIXED RT BY genotype medication timepoint
/FIXED=genotype*medication genotype medication | SSTYPE(3)
/RANDOM=timepoint | COVTYPE(VC)
/REPEATED=medication*timepoint | SUBJECT(id) COVTYPE(CS).

I would really appreciate if someone could help here :)


1 Answer 1


(I don't know if it is proper to answer old questions, especially with a shaky answer, but here goes.)

I'm only learning mixed models myself, but I think you are not doing anything wrong. The parameter estimates are simply calculated in a way that one level of a categorical variable becomes the reference point to which every other level is compared. I think there is a way to change the reference point (at least change from last to first, not sure if you can pick it freely), but in case you want to do multiple comparisons between levels, the answer is not to change the reference point, but to do separate pairwise comparisons. In your case, it would mean adding the following row to the syntax:

/EMMEANS=TABLES(genotype*medication) COMPARE(genotype)

(or perhaps COMPARE(medication), if you prefer them shown in another order).

With EMMEANS you see the estimates in a more natural form (and not in form of effects relative to intercept) and can do pairwise comparisons between individual levels. However, if there are many comparisons, you should remember to do some kind of correction, possibly with a false discovery rate procedure (http://en.wikipedia.org/wiki/False_discovery_rate).

  • $\begingroup$ Nice answer, it is a good thing to answer old questions! $\endgroup$
    – Andy W
    Commented Jun 2, 2014 at 12:17

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.