[BioC] set.seed() in gcrma

[Zhijin Wu]

Bill
Thank you for that suggestion. We will edit gcrma to restore the seed in 
the next release.
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]]
>>
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>>
> 
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-- 
-------------------------------------------
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