[adegenet-forum] Adegenet results

[Thibaut Jombart]

Hello,

I think the result makes sense. The blue cluster seems to have a private
allele, which would create perfect discrimination. This would be stronger,
in terms of differentiating groups, than the set of alleles often present
in (blue + green) and often absent from the red cluster.

Best
Thibaut

--
Dr Thibaut Jombart
Associate Professor in Outbreak Analytics, London School of Hygiene and
Tropical Medicine
Senior Lecturer in Genetic Analysis, Imperial College London
President of RECON: repidemicsconsortium.org
https://thibautjombart.netlify.com
Twitter: @TeebzR


On Tue, 14 Jan 2020 at 11:35, Kimberly Ann McLaughlin <
kimberly.mclaughlin at northwestern.edu> wrote:

> Hello,
>
>
> I clustered some presence/absence data using DAPC but I'm getting
> unexpected results. In the presence/absence heatmap, black=presence and
> yellow=absence and clusters 2 and 3 are very similar. But in
> left_clusters.pdf, I would expect clusters 2 and 3 to be closer together
> and cluster 1 to be far away. However the clusters 1 and 2 appear to be
> close together and cluster 3 is farther away. Is there any reason why I
> might be seeing this and is there anything I can do about it?
>
>
> Thanks!
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