[BioC] increase memory size in R, problem reading 67 affy CEL files

James MacDonald jmacdon at med.umich.edu
Thu Nov 25 20:07:59 CET 2004

If I am not mistaken, R simply takes whatever memory is available under
linux (unlike win32 where you have the --max-memory-size flag), so if
you are running out of memory all you can do is get more.

And yes, justRMA() does exactly the same as ReadAffy() followed by
rma(), only without an AffyBatch that can be used for certain QC plots,



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
>>> "Dipl.-Ing. Johannes Rainer" <johannes.rainer at tugraz.at> 11/25/04
11:47 AM >>>

i want to read in 67 CEL files (hgu133plus2 chips), but i get everytime
error message: "Error: cannot allocate vector of size 709203KB"
i run R (version 2.0.1, bioconductor 1.5) on a linux workstation with 2
physical RAM and 6 GB swap space... so there should not be any problem
regarding the memory installed on the system. is there a possibility to
increase the memory that can be allocated by R?
other question: the justRMA() function, does this function exactly the
same as
ReadAffy() and then rma() ?

thanks for your help!

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