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

Matthew Hannah Hannah at mpimp-golm.mpg.de
Thu Jun 17 16:45:40 CEST 2004


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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