[BioC] set.seed() in gcrma

[Kasper Daniel Hansen]

In my opinion gcrma should _not_ play with the seed. That is  
something for the user to decide.

Kasper

On Feb 13, 2008, at 9:49 AM, Zhijin Wu wrote:

> 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
>
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