[Rd] Slow ttests in R-devel
Prof Brian Ripley
ripley at stats.ox.ac.uk
Wed Jun 4 20:31:12 MEST 2003
Are you making use of S4 classes? If so see the threads on slowness in
R-patched in the last 48 hours: R-devel will be similar to R-patched was
the last time a branch update was done.
On Wed, 4 Jun 2003, Jeff Gentry wrote:
> I've noticed that some of our Bioconductor code was running drastically
> slower under current R-devel vs. current R-patched - one example is below
> using a ttest. I have the following snippet of code that demonstrates the
> problem while avoiding "real" code that takes an extremely long time to
> finish on R-devel:
>
> library(genefilter)
> data(eset)
> eset$cov1
> z <- ttest(eset$cov1, p=0.01)
> gf <- filterfun(z)
> system.time(genefilter(eset, gf))
>
> (this requires the genefilter & Biobase packages from Bioconductor)
>
> Using R-1.7.0p I had the following output:
What is that? We do have 1.7.1 beta now.
> > data(eset)
> > eset$cov1
> [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2
> > z <- ttest(eset$cov1, p=0.01)
> > gf <- filterfun(z)
> > system.time(genefilter(eset, gf))
> [1] 41.73 2.04 44.45 0.00 0.00
>
> And using R-devel, I have:
> > data(eset)
> > eset$cov1
> [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2
> > z <- ttest(eset$cov1, p=0.01)
> > gf <- filterfun(z)
> > system.time(genefilter(eset, gf))
> [1] 80.56 4.20 85.12 0.00 0.00
>
> Any ideas what might be causing this?
>
> Thanks
> -Jeff
>
> ______________________________________________
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> https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
>
--
Brian D. Ripley, ripley at stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
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