[adegenet-forum] DaPC vs. BAPS results question

[Felipe Hernández]

Thanks Thibaut,

Here you have the image and values for each estimated K. Any advice is more
than welcome, thanks!

Best,
Felipe

> grp
$Kstat
     K=1      K=2      K=3      K=4      K=5      K=6      K=7      K=8
1494.756 1481.467 1473.864 1472.002 1470.633 1472.970 1470.754 1472.011
     K=9     K=10     K=11     K=12     K=13     K=14     K=15     K=16
1471.813 1473.632 1473.924 1476.759 1476.699 1475.433 1479.546 1481.119
    K=17     K=18     K=19     K=20     K=21     K=22     K=23     K=24
1481.292 1485.865 1488.130 1488.356 1493.552 1494.979 1501.182 1499.258
    K=25     K=26     K=27     K=28     K=29     K=30     K=31     K=32
1500.146 1504.113 1511.598 1511.550 1513.889 1516.275 1522.144 1524.733
    K=33     K=34     K=35     K=36     K=37     K=38     K=39     K=40
1528.089 1530.409 1535.778 1538.049 1541.269 1546.197 1547.656 1552.127

$stat
     K=5
1470.633



2016-12-05 10:10 GMT-05:00 Thibaut Jombart <thibautjombart at gmail.com>:

> Dear Felipe,
>
> this is always a hard question, as different methods essentially do..
> different things. The K-means in find.clusters optimizes the variance
> between groups, while BAPS maximizes a likelihood function under a
> given population genetics model. So it may be the case that you have
> ~17 demes roughly at HWE, but that only 4-5 groups are optimum in
> terms of clearly delineated groups. And this is assuming both methods
> are 'right'. They may be prone to all sorts of biases. Namely, largely
> different group variances for the K-means, and deviations from the
> original model in BAPS.
>
> Feel free to post the image (or a link to it) of the BIC for
> find.clusters if you want a 2-cents advice on the number of K to look
> at.
>
> Best
> Thibaut
>
> --
> Dr Thibaut Jombart
> Lecturer, Department of Infectious Disease Epidemiology, Imperial College
> London
> Head of RECON: repidemicsconsortium.org
> sites.google.com/site/thibautjombart/
> github.com/thibautjombart
> Twitter: @TeebzR
>
>
> On 5 December 2016 at 14:29, Felipe Hernández <fhernandeu at uc.cl> wrote:
> > Good morning,
> >
> > I wonder if you may guide me with this question (that may be pretty basic
> > surely). After a run DaPC analysis using adegenet, I'm usually getting K
> > between 4 and 5 for my dataset (480 hogs, 59 microsats, 39 sampling
> sites).
> > Maximum number of clusters tried are 40. Afterwards, I tried to estimate
> > number of clusters (spatial clustering by individuals) using another
> > software (BAPS 6.0), but I got an even higher number of estimated cluster
> > (K=17), after testing different maximum number of K's (i.e., K=5 through
> > K=20). Any clue about what's the reason of this? Maybe related to the
> > maximum number of cluster tested? Or, linkage disequilibrium between some
> > loci? Sorry if the question is really basic, but I would appreciate any
> > advice.
> >
> > Regards,
> > Felipe
> >
> > --
> > Felipe Hernández
> > Médico Veterinario (DVM), MSc.
> > PhD. Candidate
> > Interdisciplinary Ecology Program
> > School of Natural Resources and Environment
> > Wildlife Ecology and Conservation Department
> > University of Florida
> >
> > _______________________________________________
> > adegenet-forum mailing list
> > adegenet-forum at lists.r-forge.r-project.org
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>



-- 
Felipe Hernández
Médico Veterinario (DVM), MSc.
PhD. Candidate
Interdisciplinary Ecology Program
School of Natural Resources and Environment
Wildlife Ecology and Conservation Department
University of Florida
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