
Dear List,
Can anyone help me with the Agi4x44PreProcess - filtering probe function. I am not sure what I am overlooking. 
The error message says, "Error in filter.probes(aa, control = TRUE, wellaboveBG = TRUE, isfound = TRUE,  :   'targets' is missing". Does this mean, my data files do not have the filtering parameters or it does not recognize the files. 
If I specify the file name, then it is not recognizing a mandatory column eventhough it is specified in the file."Error in filter.control(ddNORM, ManuelaGO, targets, annotation.package) :   'targets' needs 'GErep' field"
I have pasted the session info for reference.
Thank you very much in advance. Bjorn
Here is the session info.
>  library("Agi4x44PreProcess")> targets=read.targets(infile="infile.txt") Target File        		FileName Treatment GErepconta 	conta.txt   control     1contb 	contb.txt   control     1contc 	contc.txt   control     1contd 	contd.txt   control     1tumora  	tumora.txt       tumor     2tumorb   	tumorb.txt       tumor     2tumorc   	tumorc.txt       tumor     2tumord  	tumord.txt       tumor     2 >  aa=read.AgilentFE(targets, makePLOT=FALSE)Read conta.txt Read contb.txt Read contc.txt Read contd.txt Read tumora.txt Read tumorb.txt Read tumorc.txt Read tumord.txt    RGList: 	dd$R:	'gProcessedSignal'  	dd$G:	'gMeanSignal'  	dd$Rb:	'gBGMedianSignal'  	dd$Gb:	'gBGUsed'   > aaFILT = filter.probes(aa, 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(aa, control = TRUE, wellaboveBG = TRUE, isfound = TRUE,  :   'targets' is missing > aaFILT = filter.probes(aa, 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="infile.txt")FILTERING PROBES BY FLAGS 
Error in filter.control(ddNORM, ManuelaGO, targets, annotation.package) :   'targets' needs 'GErep' field
Bjorn GillPh.D. Candidate in BiologyUniversity of WaterlooOntario, Canada
 		 	   		  
_________________________________________________________________


	[[alternative HTML version deleted]]

