[R] PCA error: svd(x, nu=0) infinite or missing values

[Silvia Lomascolo]

Hi,
I am trying to do a PCA on my data but I keep getting the error message

svd(x, nu=0) infinite or missing values

From the messages posted on the subject, I understand that the NAs in my

data might be the problem, but I thought na.omit would take care of that.
Less than 5% of my cells are missing data. However, the NAs are not
regularly distributed across my matrix: certain cases and variables have
most of the NAs in the data set. Might that be the problem? Any hints as to
how to resolve this without having to get rid of those cases and variables?
Code is pasted below.

Any help is greatly appreciated!

Silvia.

CODE:

ot = read.table('C:\\Documents and Settings\\...\\matrix.txt', header=T)
ot.pca = prcomp(ot, scale.=T, na.omit)#this is as far as I got. I have also
tried princomp but I get a very similar error message

I use Windows, and R version 2.6.0.

[Prof Brian Ripley]

Please read the help page:

## S3 method for class 'formula':
prcomp(formula, data = NULL, subset, na.action, ...)

## Default S3 method:
prcomp(x, retx = TRUE, center = TRUE, scale. = FALSE, tol = NULL, ...)

So there is no na.action argument for the form you used, and your
'na.omit' matches 'retx'. Try

prcomp(~ ., data=ot, na.action=na.omit, scale=TRUE)

or

prcomp(na.omit(ot), scale=TRUE)

Post by Silvia Lomascolo
Hi,
I am trying to do a PCA on my data but I keep getting the error message
svd(x, nu=0) infinite or missing values

From the messages posted on the subject, I understand that the NAs in my

data might be the problem, but I thought na.omit would take care of that.
Less than 5% of my cells are missing data. However, the NAs are not
regularly distributed across my matrix: certain cases and variables have
most of the NAs in the data set. Might that be the problem? Any hints as to
how to resolve this without having to get rid of those cases and variables?
Code is pasted below.
Any help is greatly appreciated!
Silvia.
ot = read.table('C:\\Documents and Settings\\...\\matrix.txt', header=T)
ot.pca = prcomp(ot, scale.=T, na.omit)#this is as far as I got. I have also
tried princomp but I get a very similar error message
I use Windows, and R version 2.6.0.