Dear Bjorn, I am not 100% sure but it seems the problem lies in the way you call function filter.probes. If you want to skip the argument limSAT (as you did), you will need to explicitly tell targets=targets. Trying to use targets="infile.txt" will not work. The function filter.probes expects a data frame here, not a string of file name. Hope this helps, Yong BJORN GILL wrote: > 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 = TR U! > E, 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >