[adegenet-forum] Adegenet results

[Zhian Kamvar]

The 10th allele appears to be fixed in the third population while the previous ten vary throughout. Since none of the other alleles are fixed in this manner, this one likely drives the differentiation (you can confirm it by looking at the loading plot for the first axis). 

You might consider removing that particular locus in this analysis since it appears to be driving your clustering.

Best,
Zhian

> On Jan 14, 2020, at 11:35 , adegenet-forum-request at lists.r-forge.r-project.org wrote:
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>   1. Adegenet results (Kimberly Ann McLaughlin)
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> Date: Mon, 13 Jan 2020 19:13:04 +0000
> From: Kimberly Ann McLaughlin <kimberly.mclaughlin at northwestern.edu>
> To: "adegenet-forum at lists.r-forge.r-project.org"
> 	<adegenet-forum at lists.r-forge.r-project.org>
> Subject: [adegenet-forum] Adegenet results
> Message-ID: <1578942784283.99111 at northwestern.edu>
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> 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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