Hi Leonardo, Thanks. The comments you suggested still do not work. > library (limma) > targets1 <- as.matrix(read.table("targets.txt", header = TRUE)); targets1 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" > targets2 <- matrix (c(targets1[,3], targets1[,2]),nrow=16,ncol=2); targets2 [,1] [,2] [1,] "MB72-20-12_635.txt" "MB72-20-12_532.txt" [2,] "MB72-20-13_635.txt" "MB72-20-13_532.txt" [3,] "MB72-20-14_635.txt" "MB72-20-14_532.txt" [4,] "MB72-20-15_635.txt" "MB72-20-15_532.txt" [5,] "MB72-20-16_635.txt" "MB72-20-16_532.txt" [6,] "MB72-20-17_635.txt" "MB72-20-17_532.txt" [7,] "MB72-20-18_635.txt" "MB72-20-18_532.txt" [8,] "MB72-20-19_635.txt" "MB72-20-19_532.txt" [9,] "MB72-20-20_635.txt" "MB72-20-20_532.txt" [10,] "MB72-21-02_635.txt" "MB72-21-02_532.txt" [11,] "MB72-21-03_635.txt" "MB72-21-03_532.txt" [12,] "MB72-21-04_635.txt" "MB72-21-04_532.txt" [13,] "MB72-21-05_635.txt" "MB72-21-05_532.txt" [14,] "MB72-21-06_635.txt" "MB72-21-06_532.txt" [15,] "MB72-21-07_635.txt" "MB72-21-07_532.txt" [16,] "MB72-21-08_635.txt" "MB72-21-08_532.txt" > RG <- read.imagene(targets2) Read header information Read MB72-20-12_635.txt Error in RG$Gb[, i] <- obj[, columns$b] : number of items to replace is not a multiple of replacement length ======================================== 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: [1]http://www.tcag.ca/statisticalAnalysis.html References 1. http://www.tcag.ca/statisticalAnalysis.html

Hi Pingzhao, The read.imagene command couldn't find the column assigned for background, once in your file its named "Background Mean", while the default is "Signal Median, or Signal Mean if auto segmentation has been used" (take a look at Limma User's Guide page 14), so you must set the columns for foreground (f) and background (b). The following command worked properly: RG <- read.imagene(targets2, column = list (f="Signal Mean",b="Background Mean")) 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 3:28 PM Para: bioconductor at stat.math.ethz.ch Assunto: [BioC] RES: LIMMA: load two-color data (Imagene format) Hi Leonardo, Thanks. The comments you suggested still do not work. > library (limma) > targets1 <- as.matrix(read.table("targets.txt", header = TRUE)); targets1 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" > targets2 <- matrix (c(targets1[,3], targets1[,2]),nrow=16,ncol=2); targets2 [,1] [,2] [1,] "MB72-20-12_635.txt" "MB72-20-12_532.txt" [2,] "MB72-20-13_635.txt" "MB72-20-13_532.txt" [3,] "MB72-20-14_635.txt" "MB72-20-14_532.txt" [4,] "MB72-20-15_635.txt" "MB72-20-15_532.txt" [5,] "MB72-20-16_635.txt" "MB72-20-16_532.txt" [6,] "MB72-20-17_635.txt" "MB72-20-17_532.txt" [7,] "MB72-20-18_635.txt" "MB72-20-18_532.txt" [8,] "MB72-20-19_635.txt" "MB72-20-19_532.txt" [9,] "MB72-20-20_635.txt" "MB72-20-20_532.txt" [10,] "MB72-21-02_635.txt" "MB72-21-02_532.txt" [11,] "MB72-21-03_635.txt" "MB72-21-03_532.txt" [12,] "MB72-21-04_635.txt" "MB72-21-04_532.txt" [13,] "MB72-21-05_635.txt" "MB72-21-05_532.txt" [14,] "MB72-21-06_635.txt" "MB72-21-06_532.txt" [15,] "MB72-21-07_635.txt" "MB72-21-07_532.txt" [16,] "MB72-21-08_635.txt" "MB72-21-08_532.txt" > RG <- read.imagene(targets2) Read header information Read MB72-20-12_635.txt Error in RG$Gb[, i] <- obj[, columns$b] : number of items to replace is not a multiple of replacement length ======================================== 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: [1]http://www.tcag.ca/statisticalAnalysis.html References 1. 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