[BioC] Error message with rmaMicroRna on mouse data in AgiMicroRNA
Pedro López Romero
plopez at cnic.es
Fri Jun 18 07:46:02 CEST 2010
Thanks Richard,
I am looking at the headings of your files, and it seems that the "chr_coord" it´s not present. This might not be an issue, but if the FE 10 version (or mouse data) don´t provide this column, I will have to modify the function that reads the data. Could you send me one of your files off-list?, it will help me to work on your data and see the specific problems you are posting, and I will try to fix any problem that the package might have asap.
Thanks a lot,
p.-
-----Mensaje original-----
De: Richard Friedman [mailto:friedman at cancercenter.columbia.edu]
Enviado el: Thursday, June 17, 2010 4:50 PM
Para: Pedro López Romero
CC: bio c bioconductor
Asunto: Re: Error message with rmaMicroRna on mouse data in AgiMicroRNA
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 López 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$ProbeName %in% ProbeName.rep[ii])
> cat(ii, " - ",index,"\n")
> }
>
> Let me know what u get from here.
> It might be helpful if you were able to send me a couple of your
> text files to do the checkings myself, and try to figure out where
> the problem is.
>
> p.-
>
>
> -----Mensaje original-----
> De: Richard Friedman [mailto:friedman at cancercenter.columbia.edu]
> Enviado el: Wednesday, June 16, 2010 5:18 PM
> Para: Pedro López Romero; James W. MacDonald; bio c bioconductor
> Asunto: Error message with rmaMicroRna on mouse data in AgiMicroRNA
>
> Dear Pedro, Jim, and Bioconductor List,
>
> I received an error message when trying to normalize data with
> AgiMicroRMA
>> agiMicro.rma=rmaMicroRna(agiMicroraw,
> + normalize=TRUE,
> + background=FALSE)
> Error in if (min(dd.aux$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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asume responsabilidad alguna por tales circunstancias. Si no
consintiese la utilización del correo electrónico o de las
comunicaciones vía Internet le rogamos nos lo comunique y ponga en
nuestro conocimiento de manera inmediata.
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addressed and contains privileged and confidential information
protected from disclosure by law. If you are not the addressee
indicated in this message, you should immediately delete it and any
attachments and notify the sender by reply e-mail or by phone
(+34 914531200). In such case, you are hereby notified that any
dissemination, distribution, copying or use of this message or any
attachments, for any purpose, is strictly prohibited by law. We
hereby inform you, as addressee of this message, that e-mail and
Internet do not guarantee the confidentiality, nor the completeness
or proper reception of the messages sent and, thus, CNIC does not
assume any liability for those circumstances. Should you not agree
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