[adegenet-forum] sPCA

[Jombart, Thibaut]

Hello, 

Thanks for the feedback.

You can't use the global test, or any test of spatial structure, on sPCA components, since they are already optimized for spatial structure.

The global test is meant to be performed on the raw dataset as a whole, or at least any preceding transformation should not optimize spatial structure to avoid circularity.

Best

Thibaut
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Dr Thibaut JOMBART
MRC Centre for Outbreak Analysis and Modelling
Department of Infectious Disease Epidemiology
Imperial College - Faculty of Medicine
St Mary’s Campus
Norfolk Place
London W2 1PG
United Kingdom
Tel. : 0044 (0)20 7594 3658
t.jombart at imperial.ac.uk
http://sites.google.com/site/thibautjombart/
http://adegenet.r-forge.r-project.org/

________________________________________
From: Alastair Potts [potts.a at gmail.com]
Sent: 07 July 2011 16:35
To: Jombart, Thibaut; adegenet-forum at r-forge.wu-wien.ac.at
Subject: sPCA

Hi Jombart,
You've put together a really nice vignette for sPCA (just downloaded the
most recent version). It really explains the whole thought process very
nicely.
A question: can the global test be used on an axis by axis basis? More
specifically, can one use it to test the first set of axes independently
to decide which axes to keep and which to drop? At the moment I have a
significant global test, but I'm not too sure where to stop when it
comes to dropping and retaining axes.

Cheers,
Alastair Potts