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

From: Tae-Hoon Chung <thchung_at_tgen.org>
Date: Fri 02 Jul 2004 - 09:52:24 EST

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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https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Fri Jul 02 09:57:02 2004

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