[R] R memory

[ripley@stats.ox.ac.uk]

On Tue, 15 Oct 2002, Luis Miguel Almeida da Silva wrote:

> Hello
>
> I was doing PCA (principal component analysis) with a DNA
> expression matrix (7000 rows/38 columns; from golubEsets) but I
> had the following problem
>
> "Error:cannot allocate vector of size 397051 Kb
> In addition: Warning message:
> Reached total allocation of 119Mb: see help(memory.size)"
>
> I've already done some filtering (reduced to 3051 rows) but the
> problem remains, only the size of the vector to allocate is
> smaller.
>
> Can I allocate more memory? How? Probably the problem is also
> from the machine itself, which is a Pentium III 700 Mhz 128Mb
> RAM. Could you help me?

See the rw-FAQ.

What method are you using, though?  prcomp or princomp?  princomp
works on the covariance matrix that is only 38x38, and this seems
perfectly feasible.

>
> Thanks
>
> Luis Silva
>
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-- 
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)
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