[BioC] error message in cvArray command in AgiMicroRna
Neel Aluru
naluru at whoi.edu
Fri Jun 4 21:08:03 CEST 2010
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","SystematicName",
"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]]
>
> _______________________________________________
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>
Neel Aluru
Postdoctoral Scholar
Biology Department
Woods Hole Oceanographic Institution
Woods Hole, MA 02543
USA
508-289-3607
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