[R] prcomp(X,center=F) ??

[Mark Difford]

Hi Agus,

>> But the rotation made with the eigenvectors of prcomp(X,center=F) yields 
>> axes that are correlated. Therefore, prcomp(X,center=F) is not really a
>> PCA.

cor() is not an appropriate test of whether two vectors are orthogonal. The
definition that two vectors (in an inner product space) are orthogonal is
that their inner product is zero.

## The appropriate test uses ?"%*%" to multiply the matrices:
set.seed(123)
X <- cbind(rnorm(100,100,50),rnorm(100,100,50)) 
X[,2] <- X[,1]*1.5-50 +runif(100,-70,70)
eigvcent <- prcomp(X,center=T,scaling=F)
eigvnocent <- prcomp(X,center=F,scaling=F)

eigvcent$rotation[,1] %*% eigvcent$rotation[,2]
[1,] -2.211772e-17

eigvnocent$rotation[,1] %*% eigvnocent$rotation[,2]
[1,] -1.680513e-17

In both cases, PCs 1 and 2 are orthogonal.

Regards, Mark.


alobo wrote:
> 
> I do not understand, from a PCA point of view, the option center=F
> of prcomp()
> 
> According to the help page, the calculation in prcomp() "is done by a 
> singular value decomposition of the (centered and possibly scaled) data 
> matrix, not by using eigen on the covariance matrix"   (as it's done by 
> princomp()) .
> "This is generally the preferred method for numerical accuracy"
> 
> The question is that while
> prcomp(X,center=T,scaling=F) is equivalent to princomp(X,scaling=F),
> but prcomp(X,center=F) has no equivalent in princomp()
> 
> Also, the rotation made with either the eigenvectors of 
> prcomp(X,center=T,scaling=F) or the ones of princomp(X,scaling=F)
> yields PCs with a minimum correlation, as expected
> for a PCA. But the rotation made with the eigenvectors of 
> prcomp(X,center=F) yields axes that are correlated.
> Therefore, prcomp(X,center=F) is not really a PCA.
> 
> See the following example, in which the second column of
> data matrix X is linearly correlated to the first column:
> 
>  > X <- cbind(rnorm(100,100,50),rnorm(100,100,50))
>  > X[,2] <- X[,1]*1.5-50 +runif(100,-70,70)
>  > plot(X)
>  > cor(X[,1],X[,2])
> [1] 0.903597
> 
>  > eigvnocent <- prcomp(X,center=F,scaling=F)[[1]]
>  > eigvcent <- prcomp(X,center=T,scaling=F)[[1]]
>  > eigvecnocent <- prcomp(X,center=F,scaling=F)[[2]]
>  > eigveccent <- prcomp(X,center=T,scaling=F)[[2]]
> 
>  > PCnocent <- X%*%eigvecnocent
>  > PCcent <- X%*%eigveccent
>  > par(mfrow=c(2,2))
>  > plot(X)
>  > plot(PCnocent)
>  > plot(PCcent)
> 
>  > cor(X[,1],X[,2])
> [1] 0.903597
>  > cor(PCcent[,1],PCcent[,2])
> [1] -8.778818e-16
>  > cor(PCnocent[,1],PCnocent[,2])
> [1] -0.6908334
>  >
> 
> Also the help page of prcomp() states:
> "Details
> 
> The calculation is done by a singular value decomposition of the 
> (centered and possibly scaled) data matrix..."
> 
> The parenthesis implies some ambiguity, but I do interpret the sentence 
> as indicating that the calculation should always be done using a 
> centered data matrix.
> Finally, all the examples in the help page use centering (or scaling, 
> which implies centering)
> 
> Therefore, why the option center=F ?
> 
> Agus
> 
> 
> 
> Agus
> 
> -- 
> Dr. Agustin Lobo
> Institut de Ciencies de la Terra "Jaume Almera" (CSIC)
> LLuis Sole Sabaris s/n
> 08028 Barcelona
> Spain
> Tel. 34 934095410
> Fax. 34 934110012
> email: Agustin.Lobo at ija.csic.es
> http://www.ija.csic.es/gt/obster
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> 
> 

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