[BioC] Reading 80 CEL files.

[Sean Davis]

On Nov 14, 2007 4:27 AM, Pure Lu <ppure379 at yahoo.com.tw> wrote:
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> Hello~~~
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> I am trying to read 80 HG-U133A arrays so I did as follows:
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> > memory.limit(size=4095)
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> > options(object.size=10000000000, digits=8, scipen=100, memory=3200483647, contrasts=c("contr.treatment", "contr.poly"))
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> > library(affy)
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> > cel.file <- ReadAffy(celfile.path = "D://CEL)
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> However, it showed
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> Error: cannot allocate vector of size 309.4 Mb
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> I have tried adding the --max-mem-size=2Gb tag onto my shortcut.
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> The machine has 2G RAM and a 3.30GHz processor.
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> Is there any idea to let R use more memory anywhere?

Hi, Pure.

Since the machine you are using has only 2Gb of RAM and is a Windows
machine (it appears), it is unlikely that you will be able to load all
80 of the CEL files at once using ReadAffy.  You can load then in a
few chunks if you just want to check QC measures, etc.  If you simply
want to normalize all those arrays, try using the justRMA() function,
which is much less memory-intensive than ReadAffy.

Sean