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Richard Friedman
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@richard-friedman-513
Last seen 10.2 years ago
Dear Pedro,
Thank you for your reply.
My core uses FE 10.5.1. All of the columns you mention are
present.
As I mentioned in a subsequent posting there are two extra
columns,"start" and "sequence"
which mess up the reading of the data. When they are removed the
normalization works.
So I will not be trying the diagnostics which you suggest below.
I am sending you the column headings off-list.
I can send you data (6 Mb text files) if that would be helpful.
If there is anything I can do to help you improve this important
application please let me know.
Best wishes,
Rich
On Jun 17, 2010, at 4:20 AM, Pedro L?pez Romero wrote:
> Dear Richard,
>
> AgiMicroRna has not been tested on mouse data, something that I?m
> just doing right now. It seems that I am having problems myself
> loading the data into R. What version of Agilent Feature Extraction
> are you using?. The people that usually provide me with the scanned
> data files told me that they have updated the Agilent Feature
> Extraction from version 9.5.3.1 to 10.7.3.1, and this new version
> does not give columns such as "accessions", "chr_coord", "ProbeUID",
> "gBGUsed", "gMeanSignal". Can you confirm with me if this is true?,
> Honestly, I think that it is a bit weird that the new version of the
> Extractor doesn?t give the "gMeanSignal".
>
> For your problem, try this (assuming your RGList object is named
> "dd") to check if you can get the index vector containing the
> replicated probes.
>
> ProbeName.rep = unique(dd$genes$ProbeName[duplicated(dd$genes
> $ProbeName)])
> length(ProbeName.rep )
> for(ii in 1: length(ProbeName.rep)){
> index=which(dd$genes$ProbeName %in% ProbeName.rep[ii])
> cat(ii, " - ",index,"\n")
> }
>
> Let me know what u get from here.
> It might be helpful if you were able to send me a couple of your
> text files to do the checkings myself, and try to figure out where
> the problem is.
>
> p.-
>
>
> -----Mensaje original-----
> De: Richard Friedman [mailto:friedman at cancercenter.columbia.edu]
> Enviado el: Wednesday, June 16, 2010 5:18 PM
> Para: Pedro L?pez Romero; James W. MacDonald; bio c bioconductor
> Asunto: Error message with rmaMicroRna on mouse data in AgiMicroRNA
>
> Dear Pedro, Jim, and Bioconductor List,
>
> I received an error message when trying to normalize data with
> AgiMicroRMA
>> agiMicro.rma=rmaMicroRna(agiMicroraw,
> + normalize=TRUE,
> + background=FALSE)
> Error in if (min(dd.aux$Rb) < 0) { :
> missing value where TRUE/FALSE needed
>> agiMicro.rma=rmaMicroRna(agiMicroraw,
> + normalize=TRUE,
> + background=TRUE)
> Error in if (min(dd.aux$Rb) < 0) { :
> missing value where TRUE/FALSE needed
>>
> ####################################################################
############
> My session Inforrmation is:
>
>> sessionInfo()
> R version 2.11.0 (2010-04-22)
> i386-apple-darwin9.8.0
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] AgiMicroRna_1.2.0 preprocessCore_1.10.0 affy_1.26.1
> limma_3.4.0
> [5] Biobase_2.8.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.16.0
>>
>
> ####################################################################
#####################
>
> On Jim MacDonald's advice I tried a trace with the debug command:
>
> When I run the command:
>
>
agiMicro.rma=rmaMicroRna(agiMicroraw,normalize=TRUE,background=FALSE)
> in debug mode, I see that after step:
>
> index = which(dd$genes$ProbeName %in% ProbeName.rep[ii])
> when I print index it returns
> integer(0)
> which means that the ProbeName was not found. Consequently the step
of
> median calculation returns NAs.
>
> In contrast when I run the same command with the example data
dd.micro
> then the results after
> index = which(dd$genes$ProbeName %in% ProbeName.rep[ii])
> and printing index returns values such as:
> 38 64 7162 7322 8113 8556 8883 9731
> which is basically returning the ProbeName indices.
>
> Since for my data the index retuns a zero values is that the reason
> I am getting NA in the next steps and consequently at the step
>
> if (min(dd.aux$Rb) < 0) {
> dd.aux$Rb = dd.aux$Rb + abs(min(dd.aux$Rb)) + 0.5
>
> which returns the error:
>
> Error in if (min(dd.aux$Rb) < 0) { :
> missing value where TRUE/FALSE needed
>
> It seems to me that the program is not reading in the probe name
data
> correctly.
> I am using the mouse Agilent data.
> Has the program been tested on mouse as well as human?
> Also, a possible complicating factor is that the test example with
the
> program does not include a step where
> the data is read in to form the files. The data is simply read in
from
> the data statement, so I haven't really tried the
> program on reading in a test data set.
>
> 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
> ####################################
>
> I would greatly appreciate any help or suggestions you can offer.
>
> 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
>
>
>
>
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