[BioC] plier crashes with 51 CEL files

[Adaikalavan Ramasamy]

I would just like to mention that I solved this problem. I believe it is
most likely to be related to memory issues but I have not done a
systematic investigation to justify this claim. I would also like to
thank Crispin Miller whose suggestion (via private communication) helped
me somewhat narrow down the problem.


Just one more observation that I would like to make. HGU-133 plus 2
chips have more than double the number of probesets compared to its
predecessor HGU-133A.

If the preprocessing is of order(n^2), where n is number of probesets,
then we will need 4 times the computing power to work on the same number
of arrays. But if it is of order(n^3), we need 8 times more computing
power. My recent experiences suggest the later or more extreme. Does
anyone have a more informed opinion ?

Thank you.


Regards, Adai




On Wed, 2005-03-23 at 17:01 +0000, Adaikalavan Ramasamy wrote:
> 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.
> 
> Regards, 
>