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If you don't plan to compare visual to auditory conditions with a contrast, then the combined model is inappropriate. Each modality (visual/auditory) should be tested in its own model.

If you were able to setup the model (I wasn't aware that flexible factorial could take 4 factors as previously it was limited to three factors), then you can follow the approach used here:

Complex example:
This is for a design with 18 subjects in group 1, 9 subjects in group
2, 2 group terms and 2 conditions: Start with the simpliest element,
single subject in a single condition, build its contrast, repeat for
all subjects and conditions, and then combine the ones you want.

S1G1C1=[1 zeros(1,26) 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0]
S1G1C2=[1 zeros(1,26) 1 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0]
....
Now average your G1C1 and by summing and dividing by the number of
subjects, you'd get
G1C1=[ones(1,18)/18 zeros(1,9) 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0]
and
G1C2=[ones(1,18)/18 zeros(1,9) 1 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0]
and
G2C1=[zeros(1,18) ones(1,9)/9 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0]
and
G2C2=[zeros(1,18) ones(1,9)/9 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0]

Now subtract G1C1-G1C2 AND G2C2-G2C1
G1C1-G1C2=[zeros(1,27) 0 0 1 -1 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0]
and
G2C1-G2C2=[zeros(1,27) 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0]

Now subtract these two:
Interaction contrast=[zeros(1,27) 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 -1
1 0 0 0 0 0]


Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
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On Wed, Jan 29, 2014 at 10:02 AM, Jake Thompson <[log in to unmask]> wrote:
Hello,

I am trying to set up a flexible factorial model with 4 factors: Group (2 controls and 1 patient group), Subject, Task (Visual task or Auditory Task) and Condition (Hi or Lo). I want to be able to analyze the data based on the task. The tasks were separate experiments conducted on the same subjects, however I want to be able to combine them in the model for completeness. For example, I want to be able to look the contrast: Control group1 (Hi>Lo) for the Visual task. Please let me know if my factors are arranged correctly, and if I need to set the auditory task to 0 in the contrast vectors when I am concerned with only the Visual task and vice versa for the auditory task?

Thanks,

Jake Carpenter-Thompson
MD/PhD Candidate UIUC