Message-ID: <ee90fe2b-e342-2f82-96c8-9b296940e62e@okologia.mta.hu>
Date: 2016-06-06T19:58:27Z
From: Botta-Dukát Zoltán
Subject: Permanova result interpretation
In-Reply-To: <CALUvbb_N6cd5m4ArdTtyD7vykdOqyN5C+ebd1HNyeOv+bFH89g@mail.gmail.com>
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 keltez?ssel, Tingting Chen ?rta:
> 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
>
> [[alternative HTML version deleted]]
>
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--
Botta-Duk?t Zolt?n
--------------------------------
?kol?giai ?s Botanikai Int?zet
Magyar Tudom?nyos Akad?mia
?kol?giai Kutat?k?zpont
--------------------------------
2163. V?cr?t?t, Alkotm?ny u. 2-4.
tel: +36 28 360122/157
fax: +36 28 360110
botta-dukat.zoltan at okologia.mta.hu
www.okologia.mta.hu
Zolt?n BOTTA-Duk?t
--------------------------------
Institute of Ecology and Botany
Hungarian Academy of Sciences
Centre for Ecological Research
--------------------------------
H-2163 V?cr?t?t, Alkom?ny u. 2-4.
HUNGARY
Phone: +36 28 360122/157
Fax..: +36 28 360110
botta-dukat.zoltan at okologia.mta.hu
www.okologia.mta.hu