[BioC] Error message with rmaMicroRna on mouse data in AgiMicroRNA
Pedro López Romero
plopez at cnic.es
Thu Jun 17 10:20:37 CEST 2010
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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