Hi 

I am analyzing affy data with 'justPlier()' and there are some negative values
9586 out of 427536  values

 There are some as low as 0.0002 on log2 scale(whatever the default scale of values calculated by justPlier)

The PLIER documentation mentions addition of 16 (or 32) to the low values. Is 'justPlier' supposed to that? 

Is this a bug?

Many thanks
-burak

> sessionInfo()
Version 2.3.1 (2006-06-01)
i686-pc-linux-gnu

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

other attached packages:
   plier     affy   affyio  Biobase
 "1.4.0" "1.10.0"  "1.0.0" "1.10.0"


 		
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