[R] Computing very large distance matrix

Liaw, Andy andy_liaw at merck.com
Wed Feb 25 19:51:58 CET 2004

If that's 131072 points, not 132 points, the memory needed to store that is:

> 131072^2 * 8 / 1024^3
[1] 128

That's in gigabytes.  When you have a Windows machine that has at least that
much memory, you can try to do that.  Before then, try something else.


> From: Arnav Sheth
> 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.
> Thanks,
> Arnav
> 	[[alternative HTML version deleted]]
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