**0**wrote:

Hello!

I have a dataset with three factors that each have two levels. I would like to run the full model:

~ factorA*factorB*factorC

and use the Wald test for significance, but I am having trouble interpreting the results.

I understand from the manual section 3.3 that for a standard model matrix (and since my factors only have two levels, I believe this is correct), if I had two factors factorA and factorB, I would use the following code to extract results:

results(dds, contrast=c("factorA","level1","level2"))

to get the effect of factor A for the reference level of factorB.

My first question is, if I have three factors, would the same code give me the effect of factorA for the reference levels of both factorB and factorC?

If this is true, how do I get the effect of factorA on the other combinations of levels of factorB and factorC?

I understand that to get the effect of factor A in the other level of factorB for two factors, I should use the following:

results(dds, contrast=list(c("factorAlevel2","factorBlevel2.factorAlevel2")))

If , in my three factor model, this is giving me the effect of factor A on factor B level 2 and factor C level 1, how do I get the effect of factorA on factor B level2 and factor C level 2?

Or, is there a better way to get the main effects when I have a three factor model?

Thanks for any help!

Sincerely,

Sarah GW

PhD. Candidate

Northeastern University Marine Science Center