[BioC] AgiMicroRna rmaMicriRna call fails

Thu Sep 2 18:21:28 CEST 2010

On Sep 2, 2010, at 10:22 AM, Thomas Hampton wrote:

> Not sure what I am doing wrong.
>
> Any ideas?
>
> Best,
>
> Tom
>
>> sessionInfo()
> R version 2.10.0 (2009-10-26)
> powerpc-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] grid      stats     graphics  grDevices utils     datasets   
> methods
> [8] base
>
> other attached packages:
> [1] gplots_2.7.4         caTools_1.10         bitops_1.0-4.1
> [4] gdata_2.6.1          gtools_2.6.1         AgiMicroRna_1.0.0
> [7] preprocessCore_1.8.0 affy_1.24.2          limma_3.2.1
> [10] Biobase_2.6.1
>
> loaded via a namespace (and not attached):
> [1] affyio_1.14.0 tcltk_2.10.0  tools_2.10.0
>
>
>> dd.micro=readMicroRnaAFE(targets,verbose=TRUE)
> Read US22502536_251911814270_S01_miRNA-v1_95_May07_1_1.txt
> Read US22502536_251911814270_S01_miRNA-v1_95_May07_1_2.txt
> Read US22502536_251911814270_S01_miRNA-v1_95_May07_1_3.txt
> Read US22502536_251911814270_S01_miRNA-v1_95_May07_1_4.txt
> Read US22502536_251911814270_S01_miRNA-v1_95_May07_2_1.txt
> Read US22502536_251911814270_S01_miRNA-v1_95_May07_2_2.txt
> Read US22502536_251911814270_S01_miRNA-v1_95_May07_2_3.txt
> Read US22502536_251911814270_S01_miRNA-v1_95_May07_2_4.txt
> Read kathy martin-J-july-scanrepeat/K.Martin 8x15K  
> miRNA_251911814197_S01_miRNA-v1_95_May07_1_1.txt
> Read kathy martin-J-july-scanrepeat/K.Martin 8x15K  
> miRNA_251911814197_S01_miRNA-v1_95_May07_1_2.txt
> Read kathy martin-J-july-scanrepeat/K.Martin 8x15K  
> miRNA_251911814197_S01_miRNA-v1_95_May07_1_3.txt
> Read kathy martin-J-july-scanrepeat/K.Martin 8x15K  
> miRNA_251911814197_S01_miRNA-v1_95_May07_1_4.txt
> Read kathy martin-J-july-scanrepeat/K.Martin 8x15K  
> miRNA_251911814197_S01_miRNA-v1_95_May07_2_1.txt
> Read kathy martin-J-july-scanrepeat/K.Martin 8x15K  
> miRNA_251911814197_S01_miRNA-v1_95_May07_2_2.txt
> Read kathy martin-J-july-scanrepeat/K.Martin 8x15K  
> miRNA_251911814197_S01_miRNA-v1_95_May07_2_3.txt
> Read kathy martin-J-july-scanrepeat/K.Martin 8x15K  
> miRNA_251911814197_S01_miRNA-v1_95_May07_2_4.txt
>
> RGList:
> 	dd$R:		'gTotalGeneSignal'
> 	dd$G:		'gTotalProbeSignal'
> 	dd$Rb:		'gMeanSignal'
> 	dd$Gb:		'gProcessedSignal'
>
>> class(dd.micro)
> [1] "RGList"
> attr(,"package")
> [1] "limma"
>
>
> ddTGS.rma = rmaMicroRna(dd.micro, normalize = TRUE, background = TRUE)
>
>
>> ddTGS.rma = rmaMicroRna(dd.micro, normalize = TRUE, background =  
>> TRUE)
> Error in if (min(dd.aux$Rb) < 0) { :
> missing value where TRUE/FALSE needed
>
>> ddTGS.rma = rmaMicroRna(dd.micro, normalize = TRUE, background =  
>> TRUE)
> Error in if (min(dd.aux$Rb) < 0) { :
> missing value where TRUE/FALSE needed
>
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Thomas,

	I  am not sure  if this is exactly the same problem I had 2 months  
ago, but in case it is I reproduce Pedro
Lopez Romero's reply ro my problem at that time.

#####################################################################################

from: 	plopez at cnic.es
	Subject: 	Re: [BioC] AgiMicroRNA and Extra columns in Agilent Mouse  
miRNA Microarray Release 12.0 G4471A-021828.

	Date: 	June 21, 2010 5:04:25 AM EDT

	To: 	naluru at whoi.edu, bioconductor at stat.math.ethz.ch

Hi Neel and Richard,

Thanks for your patience.

I have slitghtly modified some code in the package, basically related  
to the way read.maimages is used. I have eliminated the use of the  
"chr_coord" column in some of the output files which it was what it  
was causing problems. Before these changes are made effective in the  
library, please, try this temporal solution:

dd=read.maimages(files=targets$FileName,source="agilent",

            columns=list(Rf="gTotalGeneSignal",

Gf="gTotalProbeSignal",

                                                       Rb="gMeanSignal",

Gb="gProcessedSignal"),

other.columns=list(IsGeneDetected="gIsGeneDetected",

IsSaturated="gIsSaturated",

IsFeatNonUnifOF="gIsFeatNonUnifOL",

IsFeatPopnOL="gIsFeatPopnOL",

probe_mappings="probe_mappings",

BGKmd="gBGMedianSignal",

BGKus="gBGUsed"),

                            annotation = c( "ControlType",  
"ProbeName","GeneName"),

                            verbose=TRUE,sep="\t",quote="")

before doing anything else, please check first  that you have  
"probe_mappings" in the fifth position of "dd$other"

> names(dd$other)[5]

[1] "probe_mappings"

Then, change the name of "probe_mappings" to the name that AgiMicroRna  
uses for this variable:

> names(dd$other)[5] = "chr_coord"

Then, use the rest of the functions as usual:

ddTGS.rma = rmaMicroRna(dd, normalize = TRUE, background = FALSE)

ddPROC = filterMicroRna(ddTGS.rma,

           dd,

           control = TRUE,

           IsGeneDetected = TRUE,

           wellaboveNEG = FALSE,

           limIsGeneDetected = 50,

           limNEG = 25,

           makePLOT = FALSE,

           targets,

           verbose = TRUE)

Please, let me know if you still have any problem. Thanks

p.-
###################################################################################

I hope this help,
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