[BioC] [LIMMA] change in normexp function between limma 2.2.0 to limma 2.4.4

[Ron Ophir]

Hi,
We have a microarray experiment of cDNA of 36 spotted arrays, reference
design.
Two persons run the analysis with same code and the same data for
education purposes. One loaded limma package version
>sessionInfo()
R version 2.2.0, 2005-10-06, i386-pc-mingw32 

attached base packages:
[1] "methods"   "stats"     "graphics"  "grDevices" "utils"    
"datasets" 
[7] "base"     

other attached packages:
  limma 
"2.4.4" 
and the other
>sessionInfo()
R version 2.2.0, 2005-10-06, i386-pc-mingw32 

attached base packages:
[1] "methods"   "stats"     "graphics"  "grDevices" "utils"    
"datasets" 
[7] "base"     

other attached packages:
  limma 
"2.2.0" 

we run the following code:

targets<-readTargets()
raw <-
read.images(targets=targets,format="genepix",wt.fun=wtflags(0.1))
#genepix format
raw$genes<-readMyGAL()
png(file="densityPlotPreNormalized.png",width=800,height=400)
plotDensities(raw)
dev.off()

RGb<-backgroundCorrect(raw, method="normexp", offset=50)

png(file="densityPlotPreNormalizedBS.png",width=800,height=400)
plotDensities(RGb)
dev.off()

data<-normalizeWithinArrays(RGb) # with background substraction

png(file="densityPlotNormalized.png",width=800,height=400)
plotDensities(data)
dev.off()

> max(raw$R)
[1] 63762
> max(raw$G)
[1] 64016

for limma 2.4.4
> max(RGb$R)
[1] 6.50953e+272
> max(RGb$G)
[1] 3.146027e+248

for limma 2.2

> max(RGb_all$R)
[1] 63446.46
> max(RGb_all$G)
[1] 63820.55

Where do you the problem might be?

Thanks,
Ron

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