Seed Connectivity Design/Contrast Matrix


At risk of posting too elementary of question… I’m having trouble with what I should use as a contrast matrix for the following design matrix: seed activity (“beta” - column 1); two experimental conditions (“ISOLD” & “ISNEW” - columns 2/3 in the following; and an intercept variable (column 4).


If I’m interested in seed connectivity in ISNEW > seed connectivity in ISOLD, what would my contrast matrix look like? [0 -1 1 0] would not take into account the seed connectivity, correct?



I think that you can implement that by introducing betaISOLD and betaISNEW, and contrasting their effects.

That makes sense… so only having (beta x ISOLD, beta x ISNEW, CONSTANT) with a [-1,1,0] contrast matrix?

Yes, I would do so.