[BioC] Correlation works, but dist() runs out of memory

Daniel Brewer daniel.brewer at icr.ac.uk
Tue Mar 13 16:34:18 CET 2007


I am attempting to do plot a hierarchical clustering dendogram of a
reasonable modestly sized gene expression matrix of 22011 x 16.

If I choose to use a correlation measure it works fine (
c2 <- cor(ExonExpr)
d2 <- as.dist(1-c2)
hier2 <- hclust(d2,method="average")
).  If I try to create a Euclidean distance object it crashes out with a
memory error (
> Error in vector("double", length) : vector size specified is too large
).

This seems strange as I have 3GB ram, which I would think is plenty. Any
ideas what is going wrong or how to get round this.


Thanks

Dan

PS Running R 2.4.1, Bioconductor 0.9 on SUSE 10.2 Linux.

-- 
**************************************************************
Daniel Brewer, Ph.D.

Institute of Cancer Research
Email: daniel.brewer at icr.ac.uk
**************************************************************

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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