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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