MGPCA & Discriminant Analysis

From: Alexandra Lima (
Date: Tue May 25 2004 - 12:38:05 MEST

I'm a portuguese biology student and I'm learning to use the program ADE.

I would like to do a MGPCA - Multiple Group Principal Components Analysis
(Thorpe, 1988), as I'm interested in removing a "size effect", but I'm not
sure if this is possible with ADE.

In the article "The ade4 package" (by Daniel Chessel, Anne B Dufour and Jean
Thioulouse) they say:
"Opposite to between-class analyses are within-class analyses, corresponding
to diagrams (X − YD−1
w YtDX, Q,D) (within function). These analyses extend to any type of
variables the Multiple
Group Principal Component Analysis (MGPCA,[Thorpe, 1983a])..."

But ADE presents two options:"Within group normalized PCA" of the module PCA
and "Within Analysis" of the module Discrimin. Does any one can tell me
wich one should I use ?

Just one more question:
is there a way to do a discriminant analysis in ADE not using all the
principal components calculated first with a within PCA?
This idea comes from an article (Lynch) where they do a "size in" analysis
with all the principal components and a "size out" analysis without the
first principal component.

Hope you can help me!
And thank you all for your time!

Alexandra Lima

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