Dear BioC users, I have a question regarding filter.probes function in Agi4x44PreProcess. I am analyzing few Agilent 4x44 zebrafish arrays and cannot get function work. I went through the mailing lists for this package as well as AgiMicroRna package. I have seen previously some users have asked questions about filtering probes function. The error message I am getting suggests that some columns are missing in my files. I looked at my files but cannot tell which one is missing as I don't know what this package is looking for. Any help will be highly appreciated. I have pasted the details below. Thank you Neel R version 2.11.1 (2010-05-31) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 [R.app GUI 1.34 (5589) x86_64-apple-darwin9.8.0] > library("Agi4x44PreProcess") > targets=read.targets(infile="targets2.txt") Target File FileName Treatment GErep 103-AHRR-a1 103-AHRR-a1.txt AHRRa 1 103-AHRR-a2 103-AHRR-a2.txt AHRRa 1 103-AHRR-b1 103-AHRR-b1.txt AHRRb 2 103-AHRR-b2 103-AHRR-b2.txt AHRRb 2 102-CONT-1 102-CONT-1.txt CONT 3 102-CONT-2 102-CONT-2.txt CONT 3 > dd2=read.AgilentFE(targets, makePLOT=FALSE) Read 103-AHRR-a1.txt Read 103-AHRR-a2.txt Read 103-AHRR-b1.txt Read 103-AHRR-b2.txt Read 102-CONT-1.txt Read 102-CONT-2.txt RGList: dd$R: 'gProcessedSignal' dd$G: 'gMeanSignal' dd$Rb: 'gBGMedianSignal' dd$Gb: 'gBGUsed' > dim(dd2) [1] 44407 6 > names(dd2) [1] "R" "G" "Rb" "Gb" "targets" "genes" "other" > CV.rep.probes(dd2,"zf.db",foreground="MeanSignal", raw.data=TRUE,writeR=FALSE,targets) ------------------------------------------------------ Non-CTRL Replicated probes foreground: MeanSignal FILTERING BY ControlType FLAG RAW DATA: PROBES AFTER ControlType FILTERING: 42990 ------------------------------------------------------ REPLICATED NonCtrl Probes 21495 UNIQUE probes 21495 DISTRIBUTION OF REPLICATED NonControl Probes reps 1 21495 # REPLICATED (redundant) probeNames 21495 ------------------------------------------------------ MEDIAN % CV 103-AHRR-a1 103-AHRR-a2 103-AHRR-b1 103-AHRR-b2 102-CONT-1 102-CONT-2 2.477 1.279 1.454 2.157 1.689 1.342 ------------------------------------------------------ > genes.rpt.agi(dd2,"zf.db",raw.data=TRUE,WRITE.html=FALSE,REPORT=FALSE) GENE SETS: same genes interrogated by different probes FILTERING BY ControlType FLAG RAW DATA: PROBES AFTER ControlType FILTERING: 42990 INPUT DATA: RAW CHIP: zf.db PROBE SETS (NON-CTRL prob rep. x 10): 21495 GEN-SETS (REPLICATED GENES): 2281 PROBES in gen-sets: 5012 > ddNORM=BGandNorm(dd2, BGmethod="half",NORMmethod="quantile",foregrou nd="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 ------------------------------------------------------ > ddFILT=filter.probes(ddNORM, control=TRUE,wellaboveBG=TRUE, isfound=TRUE,wellaboveNEG=TRUE,sat=TRUE,PopnOL=TRUE,NonUnifOL=T, nas=T RUE,limWellAbove=75,limISF=75,limNEG=75,limPopnOL=75,limNonUnifOL=75, limNAS=100,makePLOT=F,annotation.package="zf.db",flag.counts=T, targets=targets) FILTERING PROBES BY FLAGS FILTERING BY ControlType FLAG Error in data.frame(PROBE_ID, as.character(probe.chr), as.character(probe.seq), : arguments imply differing number of rows: 42990, 0 Neel Aluru Postdoctoral Scholar Biology Department Woods Hole Oceanographic Institution Woods Hole, MA 02543 USA 508-289-3607