Question: LIMMA: load two-color data (Imagene format)
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gravatar for pingzhao Hu
12.0 years ago by
pingzhao Hu210
pingzhao Hu210 wrote:
Hi, I have a two-colour data generated by Imagene image analysis. I have a trouble in loading the data to do normalization using limma. > library(limma) > targets<-readTargets("targets.txt") > targets SlideNumber FileNameCy3 FileNameCy5 1 12 MB72-20-12_532.txt MB72-20-12_635.txt 2 13 MB72-20-13_532.txt MB72-20-13_635.txt 3 14 MB72-20-14_532.txt MB72-20-14_635.txt 4 15 MB72-20-15_532.txt MB72-20-15_635.txt 5 16 MB72-20-16_532.txt MB72-20-16_635.txt 6 17 MB72-20-17_532.txt MB72-20-17_635.txt 7 18 MB72-20-18_532.txt MB72-20-18_635.txt 8 19 MB72-20-19_532.txt MB72-20-19_635.txt 9 20 MB72-20-20_532.txt MB72-20-20_635.txt 10 2 MB72-21-02_532.txt MB72-21-02_635.txt 11 3 MB72-21-03_532.txt MB72-21-03_635.txt 12 4 MB72-21-04_532.txt MB72-21-04_635.txt 13 5 MB72-21-05_532.txt MB72-21-05_635.txt 14 6 MB72-21-06_532.txt MB72-21-06_635.txt 15 7 MB72-21-07_532.txt MB72-21-07_635.txt 16 8 MB72-21-08_532.txt MB72-21-08_635.txt > files<-as.matrix(targets[,c("FileNameCy3","FileNameCy5")]) > RG<-read.maimages(files, source="imagene") Read header information Read MB72-20-12_532.txt Error in RG$Gb[, i] <- obj[, columns$b] : number of items to replace is not a multiple of replacement length > sessionInfo() R version 2.6.0 (2007-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] tcltk stats graphics grDevices utils datasets methods base other attached packages: [1] MANOR_1.10.0 GLAD_1.12.0 aws_1.3-3.1 limma_2.12.0 loaded via a namespace (and not attached): [1] tools_2.6.0 Thanks, Pingzhao ======================================== Pingzhao Hu Statistical Analysis Facility The Centre for Applied Genomics (TCAG) The Hospital for Sick Children Research Institute MaRS Centre - East Tower 101 College Street, Room 15-705 Toronto, Ontario, M5G 1L7, Canada Tel.: (416) 813-7654 x6016 Email: phu at sickkids.ca Web: http://www.tcag.ca/statisticalAnalysis.html
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ADD COMMENTlink modified 12.0 years ago by Leonardo Rocha40 • written 12.0 years ago by pingzhao Hu210
Answer: LIMMA: load two-color data (Imagene format)
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gravatar for Leonardo Rocha
12.0 years ago by
Leonardo Rocha40 wrote:
Hello Pingzhao, Try the following commands: library (limma) targets <- readTargets ("targets.txt"); targets targets1 <- as.matrix(read.table("targets.txt", header = TRUE)); targets1 targets2 <- matrix (c(targets1[,3], targets1[,2]),nrow=16,ncol=2); targets2 RG <- read.imagene(targets2) show (RG) I hope it helps. Leonardo -----Mensagem original----- De: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] Em nome de pingzhao Hu Enviada em: Tuesday, November 27, 2007 2:45 PM Para: bioconductor at stat.math.ethz.ch Assunto: [BioC] LIMMA: load two-color data (Imagene format) Hi, I have a two-colour data generated by Imagene image analysis. I have a trouble in loading the data to do normalization using limma. > library(limma) > targets<-readTargets("targets.txt") > targets SlideNumber FileNameCy3 FileNameCy5 1 12 MB72-20-12_532.txt MB72-20-12_635.txt 2 13 MB72-20-13_532.txt MB72-20-13_635.txt 3 14 MB72-20-14_532.txt MB72-20-14_635.txt 4 15 MB72-20-15_532.txt MB72-20-15_635.txt 5 16 MB72-20-16_532.txt MB72-20-16_635.txt 6 17 MB72-20-17_532.txt MB72-20-17_635.txt 7 18 MB72-20-18_532.txt MB72-20-18_635.txt 8 19 MB72-20-19_532.txt MB72-20-19_635.txt 9 20 MB72-20-20_532.txt MB72-20-20_635.txt 10 2 MB72-21-02_532.txt MB72-21-02_635.txt 11 3 MB72-21-03_532.txt MB72-21-03_635.txt 12 4 MB72-21-04_532.txt MB72-21-04_635.txt 13 5 MB72-21-05_532.txt MB72-21-05_635.txt 14 6 MB72-21-06_532.txt MB72-21-06_635.txt 15 7 MB72-21-07_532.txt MB72-21-07_635.txt 16 8 MB72-21-08_532.txt MB72-21-08_635.txt > files<-as.matrix(targets[,c("FileNameCy3","FileNameCy5")]) > RG<-read.maimages(files, source="imagene") Read header information Read MB72-20-12_532.txt Error in RG$Gb[, i] <- obj[, columns$b] : number of items to replace is not a multiple of replacement length > sessionInfo() R version 2.6.0 (2007-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] tcltk stats graphics grDevices utils datasets methods base other attached packages: [1] MANOR_1.10.0 GLAD_1.12.0 aws_1.3-3.1 limma_2.12.0 loaded via a namespace (and not attached): [1] tools_2.6.0 Thanks, Pingzhao ======================================== Pingzhao Hu Statistical Analysis Facility The Centre for Applied Genomics (TCAG) The Hospital for Sick Children Research Institute MaRS Centre - East Tower 101 College Street, Room 15-705 Toronto, Ontario, M5G 1L7, Canada Tel.: (416) 813-7654 x6016 Email: phu at sickkids.ca Web: http://www.tcag.ca/statisticalAnalysis.html _______________________________________________ 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
ADD COMMENTlink written 12.0 years ago by Leonardo Rocha40
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