AgiMicroRna rmaMicriRna call fails
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@thomas-hampton-2820
Last seen 10.3 years ago
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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@richard-friedman-513
Last seen 10.3 years ago
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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor 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
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