[BioC] win 64bit and general BioC computing power?

James MacDonald jmacdon at med.umich.edu
Thu Jun 17 16:58:36 CEST 2004

On Windows this is a moot point at present. The 64 bit version is still
in beta testing, so if you want to use a 64 bit OS, you will have to use
a *nix of some sort.



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

>>> "Matthew  Hannah" <Hannah at mpimp-golm.mpg.de> 06/17/04 10:45AM >>>

This has been discussed before, but please humour me and let me know
your opinions.

Currently I have 2Gz and 1GB RAM, win2k.

I understand that 64bit R/BioC is only available for Linux at present,
I currently install
R using the win32.exe build and libraries provided, when is it likely
that win64.exe 
will be available, or it is possible to source build (not that I really
understand what 
that means or if it is difficult..). More general is windows really
64bit, does this
help with things like running out of memory in excel? Or would a good
32bit processor
be the better buy?

Thanks to the justGCRMA team I can now process the 60 affy chips I need
to, but this 
may in the next year go to 120. I guess I'd like to be able to
ReadAffy, gcrma, 
fitaffyPLM and use LIMMA certainly with 60, but hopefully with more,
without it being
painfully slow.

I'd like to be able to use various clustering methods, I've tried with
hclust but it
runs out of memory with more than several thousand genes (there's 23k
on the chip).
I've heard that hierarchical clustering is not feasible on such large
amounts of genes
due to the exponential increase in memory usage - is this true, how
much RAM would you
need for 23k genes, 60-100 chips?

When using some functions, such as 4 x 4 display of image plots of
AffyPLM or scatter-
plots of multiple chip comparisons, they can take an age to display. As
BioC is mostly
2D, would a good graphics card have much effect or is it just a
processor/RAM thing, and
leave the graphics cards for gamers?

Generally I just want a faster machine as in the long term, not having
to wait so much
would save a lot. But I want to upgrade to something without finding it
is not 
up to the job in 6 months or a year. I use too many general windows
programs, and I'm
networked so I don't really want to move away from windows unless
there's a huge gain to
be made...

So, what would you consider before deciding...


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