[FieldTrip] Calculation of within-subject interaction

[mapaul at uni-osnabrueck.de]

Dear fieldtrip community,

I found this very helpful tutorial on how to calculate an interaction
effect using a cluster-based permutation:

http://www.fieldtriptoolbox.org/faq/how_can_i_test_an_interaction_effect_using_cluster-based_permutation_tests

I have a question regarding this step:

Copy GA11 to GAdiff11_12 and perform the assignment
GAdiff11_12.avg=GA11.avg-GA12.avg.
Copy GA21 to GAdiff21_22 and perform the assignment
GAdiff21_22.avg=GA21.avg-GA22.avg.

I have a full within-subjects design and I was wondering if it matters
which of my factors I define as factor 1 and which as factor 2. In other
words, is there a difference between calculating

GA11.avg - GA12.avg followed by GA21.avg - GA22.avg
as opposed to GA11.avg - GA21.avg followed by GA12.avg - GA22.avg

and then running a permutation test on the differences?

Any help would be greatly appreciated!

Thanks and with best regards,
Mariella