[BioC] normexp

[Yolande Tra]

Hi everyone,
 
Please, I need some help for the following.
I have 11 output files where some of the intensities are 0 (foreground and background). I tried to adjust by writing
 
for (j in 1:k) {
+  for (i in 1: n) {
+ if (RG$R[i,j]<=0) RG$R[i,j]<-150
+ if (RG$G[i,j] <=0) RG$G[i,j]<-200} }
 
(150 and 200) are arbitrary values.
 
Some of the background intensity values are larger than the foreground intensity so to have positive corrected intensity, I used

 RG <- backgroundCorrect(RG, method="normexp", offset=100)
Corrected array 1 
Corrected array 2 
Corrected array 3 
Corrected array 4 
Corrected array 5 
Corrected array 6 
Corrected array 7 
Corrected array 8 
Corrected array 9 
Corrected array 10 
Corrected array 11 
Warning message:
NaNs produced in: log(x) 
 
It seems that it stills gets zero value. Why would log(x) appears at this stage? 
I then normalize to see the print-tip loess plot.
MA <- normalizeWithinArrays(RG, RG$printer,method="printtiploess",weights=RG$weights, span= 0.5, iterations=10)
plotPrintTipLoess(MA[,3])
Attached is the plot. The normalization was not successful.
 
Yolande
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