From ripley at stats.ox.ac.uk  Wed May 17 21:02:40 2006
From: ripley at stats.ox.ac.uk (ripley at stats.ox.ac.uk)
Date: Wed, 17 May 2006 21:02:40 +0200 (CEST)
Subject: [Rd] prcomp: problem with zeros? (PR#8870)
Message-ID: <20060517190240.0A383494DA@slim.kubism.ku.dk>

On Wed, 17 May 2006, juha.heljoranta at iki.fi wrote:

> Full_Name: Juha Heljoranta
> Version: R 2.1.1 (2005-06-20)

Not a current version of R.

> OS: Gentoo Linux
> Submission from: (NULL) (88.112.29.250)
>
> 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.

> My code and temporary workaround:
>
>
>  m = matrix(...
>  ...
>  prcomp(m, center = TRUE, scale = TRUE)
>  Error in svd(x, nu = 0) : infinite or missing values in 'x'
>
>
>  m = matrix(...
>  ...
>  # ugly work around
>  m = m + 1e-120
>  # too small values will not work
>  # m = m + 1e-150
>  prcomp(m, center = TRUE, scale = TRUE)
>  # success
>
>
> The matrix in question is ~1024x13000 containing double values, thus totaling of
> ~103M of raw data. I can put it online if needed.
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595



[Rd] prcomp: problem with zeros? (PR#8870)
ripley at stats.ox.ac.uk