[BioC] Error message with rmaMicroRna on mouse data in AgiMicroRNA

[Richard Friedman]

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