[BioC] Memory error in Mac OS X Aqua GUI v1.01 with cluster package functions

[James W. MacDonald]

Betty Gilbert wrote:
> I'm sorry if the answer to my problem is buried in the archives. I have 
> limited experience with R  and I couldn't find a solution to my 
> particular problem. I am running  Mac OS X Aqua GUI v1.01 on a new G5 
> running os 10.3.8 with a 1.8Ghz processor and 1GB of sdram. I just 
> downloaded bioconducter a week ago and I'm trying to cluster a matrix I 
> created with a simulation with dimensions
> dim(nca35)
> [1] 10481    12

Making the assumption that you are simulating microarray data, I don't 
see the purpose of clustering such a large set of data. The usual 
approach is to whittle the data down to those genes thought to be 
'important' based on some metric, and then to cluster this smaller 
subset. See the genefilter package for some examples.

If you were to post this sort of message on R-help, someone who knows 
more about the bits and bytes of computers than I would probably 
calculate how much memory the distance matrix would require for this 
object. I believe it would end up being something like this:

10481*10481*8bytes = 0.94 Gb, which means it would take all but 6% of 
your RAM just to hold your dist matrix in memory, so you need more 
memory to do this.


> 
> with size
> 
>>  object.size(nca352)
> 
> [1] 1426204
> 
> I checked my ulimits variable on the unix terminal and it says it's 
> unlimited as does
> 
>>  mem.limits()
> 
> nsize vsize
>    NA    NA
> But I'm still getting errors like the following with funtions in the 
> cluster package
> 
>>  daisy(nca352, metric= "euclidean", stand=FALSE)->dnca35

daisy() is designed for clustering variables of mixed types. However, 
your data are all numeric, so this is probably not the method you want. 
If you really want to do all rows, you may be able to get by with 
clara(), which is designed for clustering large objects such as this.

Jim


> 
> Error: cannot allocate vector of size 858213 Kb
> *** malloc: vm_allocate(size=878813184) failed (error code=3)
> *** malloc[599]: error: Can't allocate region
> if it helps i also checked
> 
>>  gc()
> 
>          used (Mb) gc trigger   (Mb)
> Ncells 448662 12.0     741108   19.8
> Vcells 847630  6.5  135357901 1032.7
> 
> I tried the suggested unix command in the memory help doc but that 
> doesn't work in the Aqua GUI. Can someone tell me how to change the 
> Vcells? Although to the best of my understanding (which is limited) I 
> shouldn't have to do that. Any suggestions would be greatly appreciated.
> thanks,
> betty


-- 
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