[R] Computing very large distance matrix
tblackw at umich.edu
Wed Feb 25 19:48:00 CET 2004
A suggestion I have made in the past is to run Chris Fraley
and Adrian Raftery's mclust() procedure instead of Rousseuw's
agnes(), if you are willing to use a different clustering method.
The pdf instruction manual for the mclust package includes
explicit suggestions for how to use mclust with large data sets.
Naive attempts are guaranteed to fail, so DO read the manual.
- tom blackwell - u michigan medical school - ann arbor -
On Wed, 25 Feb 2004, Arnav Sheth wrote:
> Hello All,
> I have a 131072x132 matrix for which I need to compute a regular euclidean distance matrix, which I then need to transform and run agnes() on this transformed matrix. I am having trouble computing the distance matrix as it is fairly large and I am sure I have gone over the max.
> The specific error I am getting is:
> Error in vector("double", length) : negative length vectors are not allowed
> I have increased the memory limit to the maximum capacity of my hard drive (which is around 20gb), with no success.
> I am running the RGUI on Windows XP with 512 mb of RAM.
> Would anyone have any suggestions as to how I can overcome this problem? I would be most grateful for any help.
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