[BioC] Error Message with RMA normalization in AgiMicroRNA
Richard Friedman
friedman at cancercenter.columbia.edu
Tue Jun 8 22:56:52 CEST 2010
Jim and List,
On Jun 8, 2010, at 9:15 AM, James W. MacDonald wrote:
> Hi Richard,
>
> Richard Friedman wrote:
>> Dear Bioconductor List,
>> I received an error message when trying to normalize data with
>> AgiMicroRMA
>> > agiMicro.rma=rmaMicroRna(agiMicroraw,
>> + normalize=TRUE,
>> + background=FALSE)
>> Error in if (min(dd.aux$Rb) < 0) { :
>> missing value where TRUE/FALSE needed
>> > agiMicro.rma=rmaMicroRna(agiMicroraw,
>> + normalize=TRUE,
>> + background=TRUE)
>> Error in if (min(dd.aux$Rb) < 0) { :
>> missing value where TRUE/FALSE needed
>
> It looks like you have some NA values in agiMicroraw$Rb, so I would
> check that first. I don't see any code in rmaMicroRna() to
> gracefully handle missing data, so that is likely the problem.
I didn't see any NAs in Rb but the maximum value of Rb was was 65535
whereas the mean and median were 51 and 168 respectively.
Does this seem like a saturation effect?
If so can mess up the program?
Also I note negative values for $R.
Can this mess up the program?
>
> If there aren't any NA values in agiMicroraw$Rb, then you should try
> debuggind rmaMicroRna() to see where things are going wrong. Simply
> start with
>
> debug(rmaMicroRna)
>
> and then
>
> agiMicro.rma <- rmaMicroRna(agiMicroraw, TRUE, FALSE)
>
> you will then go into the browser, and can step through the function
> until you get to
>
> ProbeName.rep = unique(dd$genes$ProbeName[duplicated(dd$genes
> $ProbeName)])
> dd.aux = dd[1:length(ProbeName.rep), ]
>
> at which time you can look for NA values in dd.aux$Rb, and try to
> track down where they come from. But looking at the code, I don't
> see any obvious way for them to be produced if not already there.
Pasting from session:
######################################################################################
debug: dd.aux = dd[1:length(ProbeName.rep), ]
Browse[2]> dd.aux$Rb
Error: object 'dd.aux' not found
######################################################################################
For some reason dd.aux was nor created. Can that be the problem?
Thankls and best wishes,
Rich
>
> Best,
>
> Jim
>
>
>> >
>> ################################################################################
>> My session Inforrmation 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
>> >
>> ################################################################################
>> My session up to the attempt to normalize is:
>> #################################################################################
>> > 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$Gb: 'gProcessedSignal'
>> > agiMicro.rma=rmaMicroRna(agiMicroraw,
>> + normalize=TRUE,
>> + background=FALSE)
>> Error in if (min(dd.aux$Rb) < 0) { :
>> missing value where TRUE/FALSE needed
>> ################################################################################
>> 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,
>> George Scithers
>> [[alternative HTML version deleted]]
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>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
> 734-615-7826
> **********************************************************
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