[BioC] set.seed() in gcrma

[Henrik Bengtsson]

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
>
>
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>
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