[BioC] plier crashes with 51 CEL files

Adaikalavan Ramasamy ramasamy at cancer.org.uk
Wed Mar 23 18:01:50 CET 2005

Dear all,

I am trying to run the PLIER algorithm on 51 Affymetrix of HGU-133 plus
2.0 type using justPlier() function in plier package. After about 20
minutes, the process crashes with a core dump of 2 GB in size. I am
running R-2.0.1 and plier-0.03 on a Linux cluster with emulated 64-bit
processing and 10 GB of RAM.

I do very much appreciate Crispin Miller and other's work and the fact
that plier package is still in development, but this is a bit
frustrating because I am able to do RMA and GCRMA on the same dataset on
my laptop with only 512 MB of RAM. 

1) Can anyone guess why this crashes ?
2) Has anyone been successful with dataset of such size in R ?
3) Can anyone suggest alternatives ? Do you think a GCOS system on a
desktop with 4 GB RAM running Windows OS be capable of doing this ?

Thank you.


Adaikalavan Ramasamy                    ramasamy at cancer.org.uk
Centre for Statistics in Medicine       http://www.ihs.ox.ac.uk/csm/
Cancer Research UK                      Tel : 07906 308 566
Old Road Campus, Headington, Oxford     Fax : 01865 226 962

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