[R-sig-eco] Partially non-independent ANOVA?

[Cliff Beall]

Dear group-

I was wondering if someone could point me towards the correct statistical test and R-function for my situation. 

I am looking at oral bacteria and have three groups of samples, one from control subjects, and two that are derived from different sites in patients with periodontitis. So I have one totally independent group, and two that have samples that are paired.

I would like to do a test just to say that there are differences between the three groups, something like an ANOVA, but that deals with the lack of independence of the two groups.

By the way, for what I am measuring it looks like normality is a reasonable assumption but equal variances are probably not.

Thanks,

Cliff Beall
Research Assistant Professor
Division of Oral Biology
College of Dentistry
The Ohio State University
beall.3 at osu.edu