[BioC] Error Message with RMA normalization in AgiMicroRNA
James W. MacDonald
jmacdon at med.umich.edu
Tue Jun 8 23:03:19 CEST 2010
Hi Rich,
Richard Friedman wrote:
> 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$Rb) < 0) { :H
>>> missing value where TRUE/FALSE needed
>>> > agiMicro.rma=rmaMicroRna(agiMicroraw,
>>> + normalize=TRUE,
>>> + background=TRUE)
>>> Error in if (min(dd.aux$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?
Probably. At least for Affy scanners the maximum is 2^16-1, so if you
have a bunch of values at that level, I would imagine you have a
saturation problem.
> 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
Heh. In the browser, the line
debug: dd.aux = dd[1:length(ProbeName.rep), ]
means that R is just about to process that line, not that it has already
processed the line. So if you had hit enter, and then looked at
dd.aux$Rb, then it would have output a bunch of data.
Best,
Jim
> ######################################################################################
>
>
> 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]]
>>> _______________________________________________
>>> Bioconductor mailing list
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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
>> **********************************************************
>> Electronic Mail is not secure, may not be read every day, and should
>> not be used for urgent or sensitive issues
>
--
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
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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