From: <Arne.Muller_at_sanofi-aventis.com>

Date: Fri 20 Jan 2006 - 22:19:21 EST

R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Fri Jan 20 23:06:52 2006

Date: Fri 20 Jan 2006 - 22:19:21 EST

Hello,

I've implemented dynamic programming for aligning spectral data (usually 100 to 200 peaks in one spectrum, but some spectra contain > 5k peaks) entirely in R. As François Pinard pointed out, the memory usage should be proportional to the n x n dynamic programming matrix, and I've not yet had any problems on my machine (R2.2.0 win2k, 1GB mem, 2GHz Intel PV), CPU seems to be the more problematic issue.

I guess it all depends on how much data you have. You could split the dynamic programming matrix into chunks and calculate them in parallel on different machines (but the implementatino of finding the optiomal trace will probably get a bit difficult).

kind regards,

Arne

-----Original Message-----

From: r-help-bounces@stat.math.ethz.ch

[mailto:r-help-bounces@stat.math.ethz.ch]On Behalf Of Arnab mukherji
Sent: Thursday, January 19, 2006 22:55

To: r-help@stat.math.ethz.ch

Subject: [R] Dynamic Programming in R

R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Fri Jan 20 23:06:52 2006

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