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]]