[BioC] set.seed() in gcrma

[Henrik Bengtsson]

On Feb 13, 2008 9:49 AM, Zhijin Wu <zwu at stat.brown.edu> wrote:
> Bill
> Thank you for that suggestion. We will edit gcrma to restore the seed in
> the next release.

FYI, see the answer to my recent R-devel question on how to best reset the seed;

  https://stat.ethz.ch/pipermail/r-devel/2008-February/048367.html

/Henrik

> Zhijin
>
> Henrik Bengtsson wrote:
> > Hi,
> >
> > I think you have spotted something very important, and I agree that
> > the random seed should be reset by any function that set it in order
> > to get reproducible samples.  We've been working with a port/wrapper
> > for gcrma() but this never struck us - thanks for bringing it up.
> >
> > FYI, I've just sent a question to R-devel, as it is more appropriate
> > there, on how to best push the random generator back to the state it
> > was before calling set.seed().
> >
> > Best,
> >
> > Henrik
> >
> > On Feb 13, 2008 7:53 AM, William T Barry <bill.barry at duke.edu> wrote:
> >> Hello,
> >>
> >> While recently using the gcrma package, I noticed some strange behavior
> >> that I want to report.  I was applying the pre-processing algorithm (using
> >> default settings) inside a resampling scheme and noticed that subsequent
> >> calls of sample() were returning a constant vector of values. Example
> >> output shown below:
> >>
> >>> temp <- gcrma(celdat[,1:2])
> >> Adjusting for optical effect..Done.
> >> Computing affinities.Done.
> >> Adjusting for non-specific binding..Done.
> >> Normalizing
> >> Calculating Expression
> >>
> >>> sample(1:10000,3)
> >> [1] 7030 5473 8109
> >>
> >>> temp <- gcrma(celdat[,1:2])
> >> Adjusting for optical effect..Done.
> >> Computing affinities.Done.
> >> Adjusting for non-specific binding..Done.
> >> Normalizing
> >> Calculating Expression
> >>
> >>> sample(1:10000,3)
> >> [1] 7030 5473 8109
> >>
> >>> sessionInfo()
> >> R version 2.6.1 (2007-11-26)
> >> x86_64-redhat-linux-gnu
> >>
> >> locale:
> >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> >>
> >> attached base packages:
> >> [1] splines   tools     stats     graphics  grDevices utils     datasets
> >> [8] methods   base
> >>
> >> other attached packages:
> >> [1] hu6800probe_2.0.0    hu6800cdf_2.0.0      gcrma_2.10.0
> >> [4] matchprobes_1.10.0   affy_1.16.0          preprocessCore_1.0.0
> >> [7] affyio_1.6.1         Biobase_1.16.2
> >>
> >> loaded via a namespace (and not attached):
> >> [1] rcompgen_0.1-17
> >>
> >> In looking at the gcrma functions, it appears that gcrma.engine2() is
> >> setting the seed without saving and restoring .Random.seed .  This was
> >> easily corrected in the external loop of the resampling scheme, but I was
> >> unsure whether this would be considered a 'bug' in gcrma.
> >>
> >> Kind regards,
> >> Bill
> >>
> >>
> >> -------------------------------
> >> William T. Barry, Ph.D.
> >> Dept. of Biostatistics & Bioinformatics, DUMC
> >> Duke Institute for Genome Science & Policy
> >> Hock Plaza, Room 8030
> >> DUMC Box 2717
> >> Durham, NC 27710
> >>
> >> Phone: 919-681-5047
> >> Fax: 919-668-9335
> >>
> >>
> >>         [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor at stat.math.ethz.ch
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
> --
> -------------------------------------------
> Zhijin (Jean) Wu
> Assistant Professor of Biostatistics
> Brown University, Box G-S121
> Providence, RI  02912
>
> Tel: 401 863 1230
> Fax: 401 863 9182
> http://stat.brown.edu/~zwu
>
>