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

Leonardo leobernardesrocha at gmail.com
Tue Nov 27 18:00:19 CET 2007

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.


-----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)


  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)

LC_COLLATE=English_United States.1252;LC_CTYPE=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



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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