[BioC] Problems Reading Cel Files

[James MacDonald]

Hey Jeff,

It is simple to change memory allocation for R. Simply right-click the
shortcut you are using to start R and add --max-mem=<however much ram
you have>. For instance, I have --max-mem=2G. Check ?Memory for help.

If you don't have a serious amount of RAM, you will not be able to do
53 chips (for instance I am unable to process 53 U133A chips with 2Gb
RAM). You might be able to get away with justRMA or justRMA2 (devel
version) if you simply want RMA expression values.

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> "Jeff Lande" <land0038 at umn.edu> 07/22/03 05:17PM >>>
Dear List Members,

I am trying to get started by following along with the affy textual
description manual, but I'm having early problems.  I am working with
53 Cel
files, but I have been testing by attempting to load as few as two Cel
files.  In all cases, I get a similar error message.  Here's an
example:

Error: cannot allocate vector of size 83170 Kb
In addition: Warning message:
Reached total allocation of 509 Mb: see help(memory.size)

I'm a little wary of changing memory allocation without having a good
idea
about what I am doing.  I am working in a Windows NT environment.  Can
someone suggest a good course of action or a good (in-depth) resource
on
memory allocation within R?

Thanks.

Jeff Lande
University of Minnesota

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