[Rd] prcomp: problem with zeros? (PR#8870)

Jari Oksanen jari.oksanen at oulu.fi
Wed May 17 21:25:53 CEST 2006

On 17 May 2006, at 22:02, ripley at stats.ox.ac.uk wrote:

> On Wed, 17 May 2006, juha.heljoranta at iki.fi wrote:
>> prcomp has a bug which causes following error
>>    Error in svd(x, nu = 0) : infinite or missing values in 'x'
>> on a valid data set (no Infs, no missing values). The error is most 
>> likely
>> caused by the zeros in data.
> Why do you say that?  Without a reproducible example, we cannot judge 
> what
> is going on.  If you called prcomp with scale=TRUE on a matrix that 
> has a
> completely zero (or constant) column, then this is a reasonable error
> message.

Constant columns (which is a likely reason here) indeed become NaN 
after scale(), but the error message was:

Error in svd(x, nu = 0) : infinite or missing values in 'x'

and calling this 'reasonable' is stretching the limits of reason.

However, in general this is "easy" to solve:  scale() before the 
analysis and replace NaN with 0 (prcomp handles zeros).  For instance,

x <- scale(x)
x[is.nan(x)] <- 0

(and a friendly prcomp() would do this internally.)

cheers, jari oksanen
Jari Oksanen, Oulu, Finland

More information about the R-devel mailing list