Hello:
I am trying to work with a couple of microarray data sets, using
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 1
minor 8.1
year 2003
month 11
day 21
language R
In the shortcut for invoking R I have set --max-mem-size=1024M, so that I
get
> memory.limit()
[1] 1073741824
Below is an example of what keeps happening as I am working. Any suggestions
as to how I can stop running out of mermory?
> memory.size()
[1] 502904736
> log2.harvAD <- log2.harvAD[log2.harvAD$Probesets %in%
harvard.genes$probeset,]
Error: cannot allocate vector of size 49 Kb
> log2.harvAD <- log2.harvAD[,c(1,1+order(names(log2.harvAD)[-1]))]
Error: cannot allocate vector of size 49 Kb
> log2.harvAD.annot <- unlist(lapply(strsplit(names(log2.harvAD),split=":"),
+ function(L) L[1]))[-1]
> log2.harvAD$probeset <- as.character(log2.harvAD$probeset)
Error: cannot allocate vector of size 49 Kb
> memory.size()
[1] 502912536
> gc()
used (Mb) gc trigger (Mb)
Ncells 2586025 69.1 6812252 182.0
Vcells 20108076 153.5 41205530 314.4
> memory.size()
[1] 330645720
> memory.limit()/memory.size()
[1] 3.247408
> ## Try again:
> log2.harvAD <- log2.harvAD[log2.harvAD$Probesets %in%
harvard.genes$probeset,]
Error: cannot allocate vector of size 49 Kb
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