[BioC] RES: RES: LIMMA: load two-color data (Imagene format)

[Leonardo]

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
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