[adegenet-forum] Using PCA of SPCA in linear models with environmental data.

Hanan Sela dooshra at gmail.com
Thu Jul 12 13:44:47 CEST 2012

Thank you for the answer
I want to test whether space (lat+lon) has significant effect on the
genetic structure. Therefore I would like to use spatial variables in the
right side of the model. Can you suggest a better representation of the
spatial structures than lat-lon?
Thank you

On Thu, Jul 12, 2012 at 1:58 PM, Jombart, Thibaut
<t.jombart at imperial.ac.uk>wrote:

> Dear Hanan,
> this is a tricky question, and I don't think there is a single universal
> answer. Technically speaking, the only requirement is that your residuals
> are independent, so you need to make sure there is no spatial
> autocorrelation left there. Otherwise minimizing the sum of squared
> residuals is no longer the ML solution.
> The real problem relates to the interpretation, and the assumption
> implicitly made by the model. There is several reasons why spatial genetic
> patterns can occur. Your model has the form:
> genetic pattern = lat+lon + environment + residuals
> Which means that beyond linear trends, genetic patterns are due to the
> environment. It makes sense to treat spatial autocorrelation as a
> confounding factor first removed from the analysis. But lat+lon is often
> not enough to capture all spatial structures. In this respect, using PCs
> from PCA on the left side is probably better than sPCA (no need to seek
> spatial structures to remove them afterwards).
> Cheers
> Thibaut
> ________________________________________
> From: adegenet-forum-bounces at lists.r-forge.r-project.org [
> adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Hanan
> Sela [dooshra at gmail.com]
> Sent: 12 July 2012 07:34
> To: adegenet-forum at lists.r-forge.r-project.org
> Subject: [adegenet-forum] Using PCA of SPCA in linear models with
> environmental data.
> Hello all
> I am trying to estimate the major factors affecting the spatial
> distribution of wild wheat genotypes.  I am using a linear model where the
> PCA or the SPCA   first and second axis are the dependent variables and the
> environmental variables are the predictors. Additionally I am using the
> longitude and the latitude as predictors.   Since there is a spatial
> reference on the left side of the formula, I was wondering if using SPCA on
> the right side will not be a problem.
> Thank you
> Hanan

Hanan Sela Ph.D.
Curator of the Lieberman Cereal Germplasm Bank
The Institute for Cereal Crops Improvement
Tel-Aviv University
P.O. Box 39040
Tel Aviv 69978

hans at tauex.tau.ac.il
Phone: 972-3-6405773
Cell: 972-50-5727458
Fax: 972-3-6407857
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