[R] scale or not to scale that is the question - prcomp

Petr PIKAL petr.pikal at precheza.cz
Wed Aug 19 15:02:49 CEST 2009

Thank you

Duncan Murdoch <murdoch at stats.uwo.ca> napsal dne 19.08.2009 14:49:52:

> On 19/08/2009 8:31 AM, Petr PIKAL wrote:
> > Dear all
> > 


> I would say the answer depends on the meaning of the variables.  In the 
> unusual case that they are measured in dimensionless units, it might 
> make sense not to scale.  But if you are using arbitrary units of 
> measurement, do you want your answer to depend on them?  For example, if 

> you change from Kg to mg, the numbers will become much larger, the 
> variable will contribute much more variance, and it will become a more 
> important part of the largest principal component.  Is that sensible?

Basically variables are in percentages (all between 0 and 6%) except dus 
which is present or not present (for the purpose of prcomp transformed to 
0/1 by as.numeric:). The only variable which is not such is iep which is 
basically in range 5-8. So ranges of all variables are quite similar. 

What surprises me is that biplot without scaling I can interpret by used 
variables while biplot with scaling is totally different and those two 
pictures does not match at all. This is what surprised me as I would 
expected just a small difference between results from those two settings 
as all numbers are quite comparable and does not differ much.

Best regards

> Duncan Murdoch

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