<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Dear Valeria,<br>
Despite the fact I've got seeds, i.e. generation+1, I'm interested
in generation 0. I'd like to compare the PCA on the genotypes with a
DPCOA on the assigned individuals (i.e. the plants that bears seeds
and not the seeds).<br>
But otherwise, it would be simplier to perform the analysis the way
you suggest.<br>
Perhaps it doesn't change anything ... Has anybody got a previous
and similar experience ?<br>
<br>
Le 11/22/2011 6:30 PM, valeria montano a écrit :
<blockquote
cite="mid:CADEmh=t+gUTBw_sbHRvyZgdJAquqRKybgLZ8rs5V8s+RZKHueQ@mail.gmail.com"
type="cite">Dear Thibaut and Diane,
<div><br>
</div>
<div>I was thinking... considering that leaves' genotypes are
parental generation and seeds are progeny 1 and so they are
different individuals (despite the fact that the seeds are
physically all together on the same plant), maybe you could just
put any genotype as a single ind, instead of creating a
super-gen.ind-pop-object which in this case would be rather a
"gen.fam" (family, each pop is mother plant and children). If
you put them separately, you would have a lot of individuals in
a pop with a high inbreeding coefficient and overlapping
generations (light years far from HW equilibrium), but as long
as you are interested in pop structure, maybe this is better
than a pop composed by multi-related-genotyped individuals. Or
do you think it doesn't make that much difference?</div>
<div><br>
</div>
<div>(sorry for the nerdy explicit content of this post)</div>
<div>Cheers</div>
<div><br>
</div>
<div>Valeria</div>
<div><br>
<div class="gmail_quote">On 22 November 2011 11:26, Jombart,
Thibaut <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex;">Hello,<br>
<br>
yes; what you need to do is have a factor defining "plants"
and use it when constructing your genpop object, so that
leaves and seeds of a given plant will give allele
frequencies in the plant, considered as a "population" (i.e.
a group of genotypes).<br>
<br>
Then you can run multivariate analyses on the obtained
genpop.<br>
<br>
Cheers<br>
<br>
Thibaut<br>
________________________________________<br>
From: Diane Bailleul [<a moz-do-not-send="true"
href="mailto:diane.bailleul@u-psud.fr">diane.bailleul@u-psud.fr</a>]<br>
Sent: 22 November 2011 10:14<br>
To: Jombart, Thibaut<br>
Cc: <a moz-do-not-send="true"
href="mailto:adegenet-forum@r-forge.wu-wien.ac.at">adegenet-forum@r-forge.wu-wien.ac.at</a><br>
Subject: Re: [adegenet-forum] possibility to use adegenet on
seeds data<br>
<div class="HOEnZb">
<div class="h5"><br>
Hi and thanks for your answer.<br>
I've got proper genotypes for seeds and leaves. The only
difference is<br>
that I've got one leaf for each plant and several seeds
for the same<br>
plant. And the genotypes of the seeds that belong to the
same plant can<br>
be similar, or not.<br>
I'd like to perform a PCA on my data to see if there's a
genetic<br>
structuration of my big populations.<br>
If I transform each bunch of seeds per plant in a genpop
object (if I<br>
understand correctly what you suggest), will I be able
to mix these<br>
genpop objects with the leaves informations in a genind
object ?<br>
<br>
Le 11/21/2011 12:44 PM, Jombart, Thibaut a écrit :<br>
> Hello,<br>
><br>
> I know some users have used adegenet to analyse
plant data... anyone care to share his/her experience?<br>
><br>
> I am not sure about what your seed data look like.
Is it a mixture of alleles? Or do you have proper
genotypes? In the second case, then I would consider
genotypes as 'individuals' (genind object), and seeds as
'populations'. You would probably carry out most of your
analyses at a 'population' (seed level) using a genpop
object. Having a look at the vignette "adegenet-basics"
(type vignette("adegenet-basics")) may help for
genind/genpop conversions.<br>
><br>
> Cheers<br>
><br>
> Thibaut<br>
><br>
> ________________________________________<br>
> From: <a moz-do-not-send="true"
href="mailto:adegenet-forum-bounces@r-forge.wu-wien.ac.at">adegenet-forum-bounces@r-forge.wu-wien.ac.at</a>
[<a moz-do-not-send="true"
href="mailto:adegenet-forum-bounces@r-forge.wu-wien.ac.at">adegenet-forum-bounces@r-forge.wu-wien.ac.at</a>]
on behalf of Bailleul [<a moz-do-not-send="true"
href="mailto:diane.bailleul@u-psud.fr">diane.bailleul@u-psud.fr</a>]<br>
> Sent: 19 November 2011 21:45<br>
> To: <a moz-do-not-send="true"
href="mailto:adegenet-forum@r-forge.wu-wien.ac.at">adegenet-forum@r-forge.wu-wien.ac.at</a><br>
> Subject: [adegenet-forum] possibility to use
adegenet on seeds data<br>
><br>
> Good afternoon,<br>
><br>
> I'm sorry to bother you but I've read the adegenet
documentation and I can't find the answer to my
question.<br>
><br>
> I've got a data set of genotypes of plant samples
of leaves and seeds divided between different
populations.<br>
><br>
> For leaves, each genotype is an plant. But for
seeds, I've got 2 or 8 differents genotypes of 2 or 8
seeds for the same individual.<br>
><br>
> The data set is divided as followed :
populationX/plantX/seedX for seeds or populationX/plantX
for leaves.<br>
><br>
> Can I use the adegenet package to analyse my data ?
Is there is any risk that each seed will be considered
as one plant ?<br>
><br>
> Thanks for your answer,<br>
><br>
> Diane<br>
><br>
<br>
<br>
--<br>
Diane Bailleul<br>
Doctorante<br>
Université Paris-Sud 11 - Faculté des Sciences d'Orsay<br>
Unité Ecologie, Systématique et Evolution<br>
Département Biodiversité, Systématique et Evolution<br>
UMR 8079 - UPS CNRS AgroParisTech<br>
Porte 320, premier étage, Bâtiment 360<br>
91405 ORSAY CEDEX FRANCE<br>
(0033) 01.69.15.56.64<br>
<br>
<br>
_______________________________________________<br>
adegenet-forum mailing list<br>
<a moz-do-not-send="true"
href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><br>
<a moz-do-not-send="true"
href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum"
target="_blank">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum</a><br>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
Diane Bailleul
Doctorante
Université Paris-Sud 11 - Faculté des Sciences d'Orsay
Unité Ecologie, Systématique et Evolution
Département Biodiversité, Systématique et Evolution
UMR 8079 - UPS CNRS AgroParisTech
Porte 320, premier étage, Bâtiment 360
91405 ORSAY CEDEX FRANCE
(0033) 01.69.15.56.64</pre>
</body>
</html>