open-discussion > RE: 3 Group ANOVA
Sep 18, 2014  10:09 AM | Ged Ridgway
RE: 3 Group ANOVA
Hi Marisol,

With three groups, the null hypothesis for the main effect of group is that all three are equal, i.e. a=b=c. Writing it like that, with two equals signs, is a helpful hint that two rows are required in the F-contrast, the a=b row is [1 -1 0] and the b=c row is [0 1 -1]. I don't think you mentioned which software you are using, but with FSL, you enter the two rows as separate t-contrasts, add an F-contrast, and then tick the box next to each t-contrast to include it in the F-contrast. With SPM, you can enter the two rows on two lines of the contrast manager interface:
[ 1 -1  0
  0  1 -1]

You can stop reading now if you want ;-) One potential source of confusion, which I mention in case you read anywhere else that the contrast should be different, is that contrasts are not uniquely defined. In the case of the two-group test that you mention, scaling the contrast (e.g. [0.5 -0.5] or [2 -2]) won't change the t- or p-values (though it will scale the contrast image). In the case of multi-row F-contrasts, it gets more complicated, as adding/subtracting (possibly scaled) rows to other rows doesn't change the F- or p-values, as long as the so-called row-space of the contrast doesn't change. That's a bit abstract, but a practical example is as follows. The a=b=c null hypothesis was effectively broken up as a=b and b=c above, where you can observe that these two equalities also imply a=c, but we could also have broken it up as a=b and a=c (with b=c being implied). The latter would give the F-contrast [1 -1 0; 1 0 -1]. You might also see versions like [2 -1 -1; -1 2 -1], or [2 -1 -1; 0 1 -1] which appears in the planned comparisons handout from the website that Giora mentioned.

If you have many groups, and want to avoid entering many rows by hand, a neat trick in MATLAB is that the main effect of group contrast for N groups can be obtained as:
diff(eye(N))
For example:
>> diff(eye(5))

ans =

-1 1 0 0 0
0 -1 1 0 0
0 0 -1 1 0
0 0 0 -1 1
which you can see tests a=b=c=d=e by splitting into a=b, b=c, c=d, d=e. (The signs of each row are reversed compared to what I started with above for the three-group case, but F-contrasts aren't affected by that, as they are always effectively two-tailed.)

All the best,
Ged

Threaded View

TitleAuthorDate
Marisol Picado Sep 17, 2014
Marisol Picado Sep 17, 2014
RE: 3 Group ANOVA
Ged Ridgway Sep 18, 2014
Marisol Picado Sep 18, 2014
Ged Ridgway Sep 18, 2014
Giora Galili Sep 17, 2014
Marisol Picado Sep 18, 2014
Giora Galili Sep 17, 2014