[R] Principal component analysis

Jonathan Baron baron at cattell.psych.upenn.edu
Mon Dec 9 11:50:04 CET 2002


On 12/09/02 11:38, Arne.Muller at aventis.com wrote:
>Dear R users,
>
>I'm trying to cluster 30 gene chips using principal component analysis in
>package mva.prcomp. Each chip is a point with 1,000 dimensions. PCA is
>probably just one of several methods to cluster the 30 chips. However, I
>don't know how to run prcomp, and I don't know how to interpret it's output.

PCA is almost certainly not what you want.  Kmeans might work (or
other functions designed for clustering).

The reason your output is limited to 30 components is (roughly)
that, once you have this many, all the other 970 are predictable
from these, because you have only 30 observations.

-- 
Jonathan Baron, Professor of Psychology, University of Pennsylvania
R page:               http://finzi.psych.upenn.edu/




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