[R] memory issues with large data set

James W. MacDonald jmacdon at med.umich.edu
Thu Sep 29 03:17:06 CEST 2005

Christina Yau wrote:
> Hi,
> I am running R on Windows.  It is a Dell Dimension with a
> 3.2 Ghz Processor and 4Gb RAM.

This question concerns a BioC package, so the correct listserv is 
bioconductor at stat.math.ethz.ch, not the R-help listserv. In the future, 
you should direct questions about BioC packages there.

You don't have enough memory to read all 97 arrays into an AffyBatch, 
not to mention doing any further processing on them. You will have to 
use justRMA() or justGCRMA() to process your data.

In addition, I don't think you can access any more than 2 Gb of RAM 
anyway without making some changes. See 2.11 of the Windows FAQ.



> When using the ReadAffy() function to read in 97 arrays, I get the
> below error messages: Error: cannot allocate vector of size 393529 
> Reached total allocation of 1024Mb: see help(memory.size)
> When I use the comman "memory.limit(size=4000)" to increase the
> memory size to the maximum available, I got a "NULL" as a response.
> I proceeded to re-run ReadAffy().  This time, I only get the first
> error message. Error: cannot allocate vector of size 393529
>> From what I've read, this is more of a problem with Windows than
>> with R.  But I am wondering if there is anything I can do, either
>> with the set up of R or Windows, to solve this problem and read the
>> data set into R using this machine.
> Thank you for your attention, Christina
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James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109

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