[BioC] R performance questions

Michael Benjamin msb1129 at bellsouth.net
Wed Dec 3 04:29:59 MET 2003

Hi, all--

I wanted to start a thread on R speed/benchmarking.  There is a nice R
benchmarking overview at http://www.sciviews.org/other/benchmark.htm,
along with a free script so you can see how your machine stacks up.

Looks like R is substantially faster than S-plus.

My problem is this: with 512Mb and an overclocked AMD Athlon XP 1800+,
running at 588 SPEC-FP 2000, it still takes FOREVER to analyze multiple
.cel files using affy (expresso).  Running svm takes a mighty long time
with more than 500 genes, 150 samples.

1) Would adding RAM or processing speed improve performance the most?
2) Is it possible to run R on a cluster without rewriting my high-level
code?  In other words,
3) What are we going to do when we start collecting terabytes of array
data to analyze?  There will come a "breaking point" at which desktop
systems can't perform these analyses fast enough for large quantities of
data.  What then?

Michael Benjamin, MD
Winship Cancer Institute
Emory University,
Atlanta, GA

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