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
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