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I have browsed around and have found mixed partial answers so I decided to give my exact situation and see if you guys could help me (really appreciated).
My data has 3 columns:

  • Before treatment (numeric)
  • After treatment (numeric)
  • Active (factor: Y/N, up to 3 actives in other cases)

I measure the response before and after treatment (which makes me think of paired t-test), but ultimately I want to know if the presence of a particular active made an impact vs placebo (or "no active" group), which makes me think of ANOVA.
I've read something about two-way repeated measures ANOVA but it doesnt quite apply since I cannot use the same subject for active vs. no active. Each subject has a before/after treatment but they are either in the active or no active groups.
So at this point I am a bit confused, should I run ANOVA on the (before-after) differences or is there some sort of "paired data" test for this kind of situation.

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  • $\begingroup$ Do you know t-test is a generalised version of ANOVA? $\endgroup$ – SmallChess Oct 26 '15 at 13:23
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    $\begingroup$ @StudentT It's the other way around; the t-test is a special form of ANOVA. It's anova that's the more general. $\endgroup$ – Glen_b Oct 26 '15 at 14:38
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I can see that you have two binary factor variables, one of which is obviously paired. In this case, the assumption of independence in ANOVA 2-way is violated, and therefore you shouldn't use it. You should try the ANOVA 2-way mixed model.

There is a nice explanation:

http://www.researchgate.net/post/Two-Way_ANOVA_or_Mixed_ANOVA

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  • $\begingroup$ Thank you for the reference @Student T, it offered a very nice explanation indeed and I was able to produce a nice R output that helped me understand the effect of my variables. $\endgroup$ – JanaC Oct 28 '15 at 12:51

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