[R] Absolute ceiling on R's memory usage = 4 gigabytes?

Kort, Eric Eric.Kort at vai.org
Fri Jul 2 15:06:36 CEST 2004

Yes, we are using the HGU-133plus2 chips with 50,000+ probes, and I suppose that the memory requirements increase geometrically as the chip size increases.
Thanks for your email...I can let you know if we have any success if you are interested for future reference.

	-----Original Message----- 
	From: Tae-Hoon Chung [mailto:thchung at tgen.org] 
	Sent: Thu 7/1/2004 7:52 PM 
	To: Kort, Eric 
	Cc: r-help at stat.math.ethz.ch 
	Subject: Re: [R] Absolute ceiling on R's memory usage = 4 gigabytes?

	Hi, Eric.
	It seems a little bit puzzling to me. Which Affymetrix chip do you use?
	The reason I'm asking this is that yesterday I was able to normalize
	150 HU-133A CEL files (containing 22283 probes) using R 1.9.1 in Mac OS
	X 10.3.3 with 1.5 GB memory. If your chip has more probes than this,
	then it must be understandable ...
	On Jul 1, 2004, at 2:59 PM, Kort, Eric wrote:
	> Hello.  By way of background, I am running out of memory when
	> attempting to normalize the data from 160 affymetrix microarrays using
	> justRMA (from the affy package).  This is despite making 6 gigabytes
	> of swap space available on our sgi irix machine (which has 2 gigabytes
	> of ram).  I have seen in various discussions statements such as "you
	> will need at least 6 gigabytes of memory to normalize that many
	> chips", but my question is this:
	> I cannot set the memory limits of R (1.9.1) higher than 4 gigabytes as
	> attempting to do so results in this message:
	> WARNING: --max-vsize=4098M=4098`M': too large and ignored
	> I experience this both on my windows box (on which I cannot allocate
	> more than 4 gigabytes of swap space anyway), and on an the above
	> mentioned sgi irix machine (on which I can).  In view of that, I do
	> not see what good it does to make > 4 gigabytes of ram+swap space
	> available.  Does this mean 4 gigabytes is the absolute upper limit of
	> R's memory usage...or perhaps 8 gigabytes since you can set both the
	> stack and the heap size to 4 gigabytes?
	> Thanks,
	> Eric
	> This email message, including any attachments, is for the
	> so...{{dropped}}
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	Tae-Hoon Chung, Ph.D
	Post-doctoral Research Fellow
	Molecular Diagnostics and Target Validation Division
	Translational Genomics Research Institute
	1275 W Washington St, Tempe AZ 85281 USA
	Phone: 602-343-8724

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