Dear list,
I have been trying to run the function "qvalue" under the package qvalue
on a vector with about 20 million values.
> asso_p.qvalue<-qvalue(asso_p.vector)
Error: cannot allocate vector of size 156513 Kb
> sessionInfo()
Version 2.3.1 (2006-06-01)
i686-pc-linux-gnu
attached base packages:
[1] "methods" "stats" "graphics" "grDevices" "utils"
"datasets"
[7] "base"
other attached packages:
qvalue
"1.1"
> gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 320188 8.6 23540643 628.7 20464901 546.5
Vcells 101232265 772.4 294421000 2246.3 291161136 2221.4
I have been told that the linux box has 4Gb of RAM, so it should be able
to do better than this.
I searched the FAQ and found some tips on increasing memory size, but
they seem to be windows specific, such as memory.size() and the
-max-mem-size flag. On my linux box R didn't recognise them.
I don't understand the meaning of max-vsize, max-nsize and max-ppsize.
Any help on how to increase the memory allocation on linux is much
appreciated.
Many thanks,
Alex
------------------------------------
Alex Lam
PhD student
Department of Genetics and Genomics
Roslin Institute (Edinburgh)
Roslin
Midlothian EH25 9PS
Phone +44 131 5274471
Web http://www.roslin.ac.uk
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