Dear Bioconductor list, I have an error message in cvArray command in AgiMicroRna: ##################################################### > cvArray(agiMicroraw,"MeanSignal",targets,verbose=TRUE) Foreground: MeanSignal FILTERING BY ControlType FLAG RAW DATA: 5729 PROBES without CONTROLS: 5436 Error in cvArray(agiMicroraw, "MeanSignal", targets, verbose = TRUE) : NOT DUPLICATED ProbeName in chip ######################################################## My session information is: ######################################################### > sessionInfo() R version 2.11.0 (2010-04-22) i386-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] AgiMicroRna_1.2.0 preprocessCore_1.10.0 affy_1.26.1 limma_3.4.0 [5] Biobase_2.8.0 loaded via a namespace (and not attached): [1] affyio_1.16.0 ######################################################### A record of my session up to the point of the error is: ######################################################### > library("AgiMicroRna") Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: limma Loading required package: affy Loading required package: preprocessCore Attaching package: 'AgiMicroRna' The following object(s) are masked from 'package:limma': readTargets > targets<-readTargets("Targets.txt",verbose=TRUE) Target File FileName Treatment GErep AxCNTx1x1x1 AxCNTx1x1x1.txt A.CNT 1 AxCNTx2x2x2 AxCNTx2x2x2.txt A.CNT 1 AxCNTx3x3x3 AxCNTx3x3x3.txt A.CNT 1 AxCNTx7x4x4 AxCNTx7x4x4.txt A.CNT 1 BxCCL4x1x1x5 BxCCL4x1x1x5.txt B.CCL4 2 BxCCL4x2x2x6 BxCCL4x2x2x6.txt B.CCL4 2 BxCCL4x3x3x7 BxCCL4x3x3x7.txt B.CCL4 2 BxCCL4x5x4x8 BxCCL4x5x4x8.txt B.CCL4 2 CxBDLx1x1x9 CxBDLx1x1x9.txt C.BDL 3 CxBDLx2x2x10 CxBDLx2x2x10.txt C.BDL 3 CxBDLx3x3x11 CxBDLx3x3x11.txt C.BDL 3 CxBDLx4x4x12 CxBDLx4x4x12.txt C.BDL 3 DxaHSCx1x1x13 DxaHSCx1x1x13.txt D.aHSC 4 DxaHSCx2x2x14 DxaHSCx2x2x14.txt D.aHSC 4 DxaHSCx3x3x15 DxaHSCx3x3x15.txt D.aHSC 4 DxaHSCx4x4x16 DxaHSCx4x4x16.txt D.aHSC 4 > agiMicroraw<-readMicroRnaAFE(targets,verbose=TRUE) Read AxCNTx1x1x1.txt Read AxCNTx2x2x2.txt Read AxCNTx3x3x3.txt Read AxCNTx7x4x4.txt Read BxCCL4x1x1x5.txt Read BxCCL4x2x2x6.txt Read BxCCL4x3x3x7.txt Read BxCCL4x5x4x8.txt Read CxBDLx1x1x9.txt Read CxBDLx2x2x10.txt Read CxBDLx3x3x11.txt Read CxBDLx4x4x12.txt Read DxaHSCx1x1x13.txt Read DxaHSCx2x2x14.txt Read DxaHSCx3x3x15.txt Read DxaHSCx4x4x16.txt RGList: dd$R: 'gTotalGeneSignal' dd$G: 'gTotalProbeSignal' dd$Rb: 'gMeanSignal' dd$Gb: 'gProcessedSignal' > class(agiMicroraw) [1] "RGList" attr(,"package") [1] "limma" > dim(agiMicroraw) [1] 5729 16 > print(names(agiMicroraw)) [1] "R" "G" "Rb" "Gb" "targets" "genes" "other" > boxplotMicroRna(log2(agiMicroraw$Rb), + maintitle='log2 Mean Signal', + colorfill= 'orange') > plotDensityMicroRna(log2(agiMicroraw$Rb), + maintitle='log2 Mean Signal') > > par(ask=TRUE) > ddaux=agiMicroraw > ddaux$G=log2(agiMicroraw$Rb) > mvaMicroRna(ddaux, + maintitle='log2 Mean Signal', + verbose=FALSE) Hit <return> to see next plot: Hit <return> to see next plot: Hit <return> to see next plot: Hit <return> to see next plot: Hit <return> to see next plot: Hit <return> to see next plot: Hit <return> to see next plot: Hit <return> to see next plot: Hit <return> to see next plot: Hit <return> to see next plot: Hit <return> to see next plot: Hit <return> to see next plot: Hit <return> to see next plot: Hit <return> to see next plot: Hit <return> to see next plot: Hit <return> to see next plot: > > rm(ddaux) > RleMicroRna(log2(agiMicroraw$Rb), + maintitle='log2 Mean Signal - RLE') > > hierclusMicroRna(log2(agiMicroraw$Rb),targets$GErep, + methdis="euclidean", + methclu="complete", + sel=TRUE,100) > > cvArray(agiMicroraw,"MeanSignal",targets,verbose=TRUE) Foreground: MeanSignal FILTERING BY ControlType FLAG RAW DATA: 5729 PROBES without CONTROLS: 5436 Error in cvArray(agiMicroraw, "MeanSignal", targets, verbose = TRUE) : NOT DUPLICATED ProbeName in chip #################################################################### I would appreciate any suggestions which you might have. Thanks and best wishes, Rich ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist, Biomedical Informatics Shared Resource Herbert Irving Comprehensive Cancer Center (HICCC) Lecturer, Department of Biomedical Informatics (DBMI) Educational Coordinator, Center for Computational Biology and Bioinformatics (C2B2)/ National Center for Multiscale Analysis of Genomic Networks (MAGNet) Room 824 Irving Cancer Research Center Columbia University 1130 St. Nicholas Ave New York, NY 10032 (212)851-4765 (voice) friedman@cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ In Memoriam, Philip Klass [[alternative HTML version deleted]]

Hi Rich, I encountered the same problem and found the answer in the mailing list. Instead of using readMicroRnaAFE command, use read.maimages. You can find my full session info in the mailing list. > dd.micro=read.maimages(targets.micro$FileName, columns=list(R="gTotalGeneSignal",G= "gTotalProbeSignal",Rb="gMeanSignal", Gb="gProcessedSignal"), annotation=c("ProbeUID","ControlType","ProbeName","GeneName","Systemat icName", "sequence", "accessions","probe_mappings", "gIsGeneDetected","gIsSaturated","gIsFeatNonUnifOL", "gIsFeatPopnOL","chr_coord","gBGMedianSignal","gBGUsed")) After this you do exactly what you did and use cvArray command. I have some difficulty in filtering probes in this package. If it works for you, could you please let me know. Thank you Neel On Jun 4, 2010, at 1:45 PM, Richard Friedman wrote: > Dear Bioconductor list, > > I have an error message in cvArray command in AgiMicroRna: > ##################################################### >> cvArray(agiMicroraw,"MeanSignal",targets,verbose=TRUE) > Foreground: MeanSignal > > FILTERING BY ControlType FLAG > > RAW DATA: 5729 > PROBES without CONTROLS: 5436 > Error in cvArray(agiMicroraw, "MeanSignal", targets, verbose = TRUE) : > NOT DUPLICATED ProbeName in chip > ######################################################## > My session information is: > ######################################################### >> sessionInfo() > R version 2.11.0 (2010-04-22) > i386-apple-darwin9.8.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] AgiMicroRna_1.2.0 preprocessCore_1.10.0 affy_1.26.1 > limma_3.4.0 > [5] Biobase_2.8.0 > > loaded via a namespace (and not attached): > [1] affyio_1.16.0 > > ######################################################### > > A record of my session up to the point of the error is: > > ######################################################### > >> library("AgiMicroRna") > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: limma > Loading required package: affy > Loading required package: preprocessCore > > Attaching package: 'AgiMicroRna' > > The following object(s) are masked from 'package:limma': > > readTargets > >> targets<-readTargets("Targets.txt",verbose=TRUE) > > Target File > FileName Treatment GErep > AxCNTx1x1x1 AxCNTx1x1x1.txt A.CNT 1 > AxCNTx2x2x2 AxCNTx2x2x2.txt A.CNT 1 > AxCNTx3x3x3 AxCNTx3x3x3.txt A.CNT 1 > AxCNTx7x4x4 AxCNTx7x4x4.txt A.CNT 1 > BxCCL4x1x1x5 BxCCL4x1x1x5.txt B.CCL4 2 > BxCCL4x2x2x6 BxCCL4x2x2x6.txt B.CCL4 2 > BxCCL4x3x3x7 BxCCL4x3x3x7.txt B.CCL4 2 > BxCCL4x5x4x8 BxCCL4x5x4x8.txt B.CCL4 2 > CxBDLx1x1x9 CxBDLx1x1x9.txt C.BDL 3 > CxBDLx2x2x10 CxBDLx2x2x10.txt C.BDL 3 > CxBDLx3x3x11 CxBDLx3x3x11.txt C.BDL 3 > CxBDLx4x4x12 CxBDLx4x4x12.txt C.BDL 3 > DxaHSCx1x1x13 DxaHSCx1x1x13.txt D.aHSC 4 > DxaHSCx2x2x14 DxaHSCx2x2x14.txt D.aHSC 4 > DxaHSCx3x3x15 DxaHSCx3x3x15.txt D.aHSC 4 > DxaHSCx4x4x16 DxaHSCx4x4x16.txt D.aHSC 4 > >> agiMicroraw<-readMicroRnaAFE(targets,verbose=TRUE) > Read AxCNTx1x1x1.txt > Read AxCNTx2x2x2.txt > Read AxCNTx3x3x3.txt > Read AxCNTx7x4x4.txt > Read BxCCL4x1x1x5.txt > Read BxCCL4x2x2x6.txt > Read BxCCL4x3x3x7.txt > Read BxCCL4x5x4x8.txt > Read CxBDLx1x1x9.txt > Read CxBDLx2x2x10.txt > Read CxBDLx3x3x11.txt > Read CxBDLx4x4x12.txt > Read DxaHSCx1x1x13.txt > Read DxaHSCx2x2x14.txt > Read DxaHSCx3x3x15.txt > Read DxaHSCx4x4x16.txt > > RGList: > dd$R: 'gTotalGeneSignal' > dd$G: 'gTotalProbeSignal' > dd$Rb: 'gMeanSignal' > dd$Gb: 'gProcessedSignal' > >> class(agiMicroraw) > [1] "RGList" > attr(,"package") > [1] "limma" >> dim(agiMicroraw) > [1] 5729 16 >> print(names(agiMicroraw)) > [1] "R" "G" "Rb" "Gb" "targets" "genes" "other" >> boxplotMicroRna(log2(agiMicroraw$Rb), > + maintitle='log2 Mean Signal', > + colorfill= 'orange') >> plotDensityMicroRna(log2(agiMicroraw$Rb), > + maintitle='log2 Mean Signal') >> >> par(ask=TRUE) >> ddaux=agiMicroraw >> ddaux$G=log2(agiMicroraw$Rb) >> mvaMicroRna(ddaux, > + maintitle='log2 Mean Signal', > + verbose=FALSE) > Hit <return> to see next plot: > Hit <return> to see next plot: > Hit <return> to see next plot: > Hit <return> to see next plot: > Hit <return> to see next plot: > Hit <return> to see next plot: > Hit <return> to see next plot: > Hit <return> to see next plot: > Hit <return> to see next plot: > Hit <return> to see next plot: > Hit <return> to see next plot: > Hit <return> to see next plot: > Hit <return> to see next plot: > Hit <return> to see next plot: > Hit <return> to see next plot: > Hit <return> to see next plot: >> >> rm(ddaux) >> RleMicroRna(log2(agiMicroraw$Rb), > + maintitle='log2 Mean Signal - RLE') >> >> hierclusMicroRna(log2(agiMicroraw$Rb),targets$GErep, > + methdis="euclidean", > + methclu="complete", > + sel=TRUE,100) >> >> cvArray(agiMicroraw,"MeanSignal",targets,verbose=TRUE) > Foreground: MeanSignal > > FILTERING BY ControlType FLAG > > RAW DATA: 5729 > PROBES without CONTROLS: 5436 > Error in cvArray(agiMicroraw, "MeanSignal", targets, verbose = TRUE) : > NOT DUPLICATED ProbeName in chip > #################################################################### > > I would appreciate any suggestions which you might have. > > Thanks and best wishes, > Rich > ------------------------------------------------------------ > Richard A. Friedman, PhD > Associate Research Scientist, > Biomedical Informatics Shared Resource > Herbert Irving Comprehensive Cancer Center (HICCC) > Lecturer, > Department of Biomedical Informatics (DBMI) > Educational Coordinator, > Center for Computational Biology and Bioinformatics (C2B2)/ > National Center for Multiscale Analysis of Genomic Networks (MAGNet) > Room 824 > Irving Cancer Research Center > Columbia University > 1130 St. Nicholas Ave > New York, NY 10032 > (212)851-4765 (voice) > friedman at cancercenter.columbia.edu > http://cancercenter.columbia.edu/~friedman/ > > In Memoriam, > Philip Klass > > > > > [[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 > Neel Aluru Postdoctoral Scholar Biology Department Woods Hole Oceanographic Institution Woods Hole, MA 02543 USA 508-289-3607