R version 4.5.0 RC (2025-04-04 r88112 ucrt) -- "How About a Twenty-Six"
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> # complete.channel-test.ssc
> library(PreProcess)
Loading required package: oompaBase
> 
> suppressWarnings( RNGversion("3.5.3") )
> set.seed(989431)
> # simulate a complete channel object
> v <- rexp(10000, 1/1000)
> b <- rnorm(10000, 60, 6)
> s <- sapply(v-b, function(x) {max(0, x)})
> ct <- ChannelType('user', 'random', 100, 100, 'fake')
> x <- CompleteChannel(name='fraud', type=ct,
+                       data=data.frame(vol=v, bkgd=b, svol=s))
> rm(v, b, s, ct)
> 
> summary(x)
Microarray type: user random 
Labeled with: fake 
[1] "fraud"
      vol                 bkgd            svol        
 Min.   :6.560e-02   Min.   :33.61   Min.   :    0.0  
 1st Qu.:2.855e+02   1st Qu.:55.95   1st Qu.:  225.7  
 Median :6.874e+02   Median :60.01   Median :  626.7  
 Mean   :1.003e+03   Mean   :59.99   Mean   :  944.6  
 3rd Qu.:1.396e+03   3rd Qu.:64.07   3rd Qu.: 1336.5  
 Max.   :1.178e+04   Max.   :85.24   Max.   :11718.9  
> 
> opar <- par(mfrow=c(2,3))
> plot(x)
> plot(x, main='Log Scale', useLog=TRUE)
> par(opar)
> 
> opar <- par(mfrow=c(2,1))
> image(x)
> par(opar)
> 
> b <- process(x, PROC.NEG.CORRECTED.SIGNAL)
> summary(b)
background-corrected signal fraud, a microarray channel object
Parent object: x 
Microarray type: user random 
Labeled with: fake 
Design size: 100 by 100 
Design information object:  
History:
	 Foreground - Background (using object: PROC.NEG.CORRECTED.SIGNAL) with parameter = 0 

    Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
  -71.28   225.68   626.71   942.73  1336.46 11718.88 
> 
> q <- process(b, PIPELINE.STANDARD)
> summary(q)
log normalized background-corrected signal fraud, a microarray channel object
Parent object: x 
Microarray type: user random 
Labeled with: fake 
Design size: 100 by 100 
Design information object:  
History:
	 Foreground - Background (using object: PROC.NEG.CORRECTED.SIGNAL) with parameter = 0 
	 Default channel processing (using pipeline: PIPELINE.STANDARD) 
	 Global normalization (using object: proc) with parameter = 0 
	 Truncated below (using object: proc) with parameter = 0 
	 Log transformation (using object: proc) with parameter = 2 

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   -Inf   7.400   8.873    -Inf   9.966  13.098 
> 
> q <- process(x, PIPELINE.MDACC.DEFAULT)
> summary(q)
log normalized signal fraud, a microarray channel object
Parent object: object 
Microarray type: user random 
Labeled with: fake 
Design size: 100 by 100 
Design information object:  
History:
	 Foreground intensity (using object: proc) with parameter = 0 
	 Global normalization (using object: proc) with parameter = 0 
	 Truncated below (using object: proc) with parameter = 25 
	 Log transformation (using object: proc) with parameter = 2 

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  4.644   7.676   8.944   8.692   9.966  13.043 
> 
> # cleanup
> rm(x, b, q, opar)
> 
> proc.time()
   user  system elapsed 
   0.64    0.06    0.68