[BioC] affy & problems with memory

Carlos J. Gil Bellosta cgb at datanalytics.com
Tue Jan 17 15:46:02 CET 2006

R does have a garbage collection mechanism. See ?gc and the references
therein. Invoking it explictly after a massive rm() just before data
reading is always a good practice.

There are ways to improve R IO performance. One of the easiest tricks
that can be performed is to reduce the precision of the numeric values
to be read (since the input file is stored as text in RAM before being
pasted --depending on the IO function being invoked, of course, but it
is the case with read.table and its cousins--).

El lun, 16-01-2006 a las 14:21 -0600, Simon Lin escribió:
> Since R doesn't seem to have a data compressing approach as well as
> cleaning
> and garbage collection mechanism, I would suggest that adding more
> RAMs into
> your computer is the only way to solve the problem (alternatively you
> can
> increase the swap/virtual memory size up to (4GB - physical mem),
> bearing
> that extremely poor system performance).


Carlos J. Gil Bellosta

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