[R] PCA - "cov.wt(z) : 'x' must contain finite values only"

[Ravi Varadhan]

The problem is the missing values.  The argument "na.action" is not active
in princomp(), which I think is a bug, even though the help page claims that
"factory fresh" default is na.omit.

So, you need to either get rid of the rows with any missing values in them,
or use a PCA code that can deal with missing values by somehow imputing
them.

Ravi.

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Ravi Varadhan, Ph.D.

Assistant Professor, The Center on Aging and Health

Division of Geriatric Medicine and Gerontology 

Johns Hopkins University

Ph: (410) 502-2619

Fax: (410) 614-9625

Email: rvaradhan at jhmi.edu

Webpage:  http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html

 

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-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On
Behalf Of Johnson, Bethany 
Sent: Tuesday, December 18, 2007 1:14 PM
To: r-help at r-project.org
Subject: [R] PCA - "cov.wt(z) : 'x' must contain finite values only"

I am trying to run PCA on a matrix (the first column and row are
headers).  There are several cells with NA's.  When I run PCA with the
following code:
______________________________________
setwd("I:/PCA")
AsianProp<-read.csv("Matrix.csv", sep=",", header=T, row.names=1)
attach(AsianProp)
AsianProp
AsianProp.pca<-princomp(AsianProp, na.omit)
_____________________________________

I get the error message:

cov.wt(z) : 'x' must contain finite values only

What am I doing wrong?  

Thanks very much!

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