[R-sig-eco] Permanova result interpretation

[Zoltan Botta-Dukat]

Dear Tingting,

If you tested an a priori grouping by adonis, you can say that these 
groups significantly different. It means that their difference is bigger 
than the random expectation (= exepected difference between random 
groups with same size).

However, PCoA and UPGMA results indicates that this is not the best 
grouping, i.e. there may be grouping where two groups are more separated.

Best wishes

Zoltan

2016.06.06. 21:32 keltezéssel, Tingting Chen írta:
> Dear list,
>
> I have did  PCoA, UPGMA cluster analysis, and adonis on my data. And I got
> no clear separation on the PCoA plot and clustering. However the Permanova
> test is giving a very small P value. In this case, can I say these two
> groups are significantly different?
>
> Thank you very much for any help.
>
> Best,
> Tingting
>
>
> Call:
> adonis(formula = mat ~ Condition, data = meta, permutations = 9999)
>
> Permutation: free
> Number of permutations: 9999
>
> Terms added sequentially (first to last)
>
>            Df SumsOfSqs  MeanSqs F.Model      R2 Pr(>F)
> Condition  1   0.23217 0.232167  6.3284 0.14606  1e-04 ***
> Residuals 37   1.35740 0.036686         0.85394
> Total     38   1.58956                  1.00000
> ---
> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> --------------------
>
> Tingting Chen
>
> PhD candidate
>
> Whistler Center for Carbohydrate Research
>
> Department of Food Science
>
> Purdue University
>
> 745 Agriculture Mall Drive
>
> West Lafayette, IN 47907
>
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>
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-- 
Botta-Dukát Zoltán
--------------------------------
Ökológiai és Botanikai Intézet
Magyar Tudományos Akadémia
Ökológiai Kutatóközpont
--------------------------------
2163. Vácrátót, Alkotmány u. 2-4.
tel: +36 28 360122/157
fax: +36 28 360110
botta-dukat.zoltan at okologia.mta.hu
www.okologia.mta.hu


Zoltán BOTTA-Dukát
--------------------------------
Institute of Ecology and Botany
Hungarian Academy of Sciences
Centre for Ecological Research
--------------------------------
H-2163 Vácrátót, Alkomány u. 2-4.
HUNGARY
Phone: +36 28 360122/157
Fax..: +36 28 360110
botta-dukat.zoltan at okologia.mta.hu
www.okologia.mta.hu