Thank you Gang,
that absolutely makes sense. I didn't think that the 'a' or 'b' values could be negative, but since they can it works out.
So in the difference analysis I assume it will assess differences in direction (e.g., activation in grp 1, deactivation in grp 2). If I want to assess differences also in magnitude (e.g., strong activation in grp 2, weaker but significant activation in grp 2), does it make sense to remove the "step" function and only do for example
-expr '(a-a_threshold) - (b-b_threshold)' ?
Thanks again,
Hedvig.