Hello,

Can anyone help me in troubleshooting the function for filtering probes. Below is the session info and I am just trying the functions in the user guide.
Thank you,

Neel

Session info.

> setwd("/Users/Neel/agilent")
>  library("Agi4x44PreProcess")
> targets=read.targets(infile="infile.txt")
 
Target File 
          X  FileName Treatment GErep
conta cont1 conta.txt   control     1
contb cont2 contb.txt   control     2
contc cont3 contc.txt   control     3
contd cont4 contd.txt   control     4
pcba   pcb1  pcba.txt       pcb     1
pcbb   pcb2  pcbb.txt       pcb     2
pcbc   pcb3  pcbc.txt       pcb     3
pcbd   pcb4  pcbd.txt       pcb     4
 
>  aa=read.AgilentFE(targets, makePLOT=FALSE)
Read conta.txt 
Read contb.txt 
Read contc.txt 
Read contd.txt 
Read pcba.txt 
Read pcbb.txt 
Read pcbc.txt 
Read pcbd.txt 
 
  RGList: 
	dd$R:	'gProcessedSignal'  
	dd$G:	'gMeanSignal'  
	dd$Rb:	'gBGMedianSignal'  
	dd$Gb:	'gBGUsed'  
 
> aaNORM = BGandNorm(aa, BGmethod = "half", NORMmethod = "quantile", foreground = "MeanSignal", background = "BGMedianSignal", offset = 50, makePLOTpre = FALSE, makePLOTpost = FALSE)
BACKGROUND CORRECTION AND NORMALIZATION  

	foreground: MeanSignal 
	background: BGMedianSignal 

	BGmethod:	 half 
	NORMmethod:	 quantile 
	OUTPUT in log-2 scale 

------------------------------------------------------ 
> aaFILT = filter.probes(aaNORM, control = TRUE, wellaboveBG=TRUE, isfound=TRUE, wellaboveNEG= TRUE, sat=TRUE, PopnOL = TRUE, NonUnifOL = TRUE, nas = TRUE, limWellAbove = 75, limISF = 75, limNEG = 75, limPopnOL = 75, limNonUnifOL = 75, limNAS = 100, makePLOT = F, annotation.package = "org.Dr.eg.db", flag.counts = TRUE, targets)
FILTERING PROBES BY FLAGS 

Error in filter.probes(aaNORM, control = TRUE, wellaboveBG = TRUE, isfound = TRUE,  : 
  'targets' is missing 


Neel Aluru
Postdoctoral Scholar
Biology Department
Woods Hole Oceanographic Institution
Woods Hole, MA 02543
USA
508-289-3607




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