[BioC] help on reading Agilent 44k 2 colour

Alberto Goldoni alberto.goldoni at segesta.pro
Wed Mar 17 10:39:22 CET 2010

Dear all,
i'm newbie in reading agilent 44k arrays.
this is my targets file:

"SlideNumber"    "FileNameCy3"    "FileNameCy5"    "Cy3"    "Cy5"
1    "prova01.txt"    "prova02.txt"    "WT"    "Mutant"
2    "prova03.txt"    "prova04.txt"    "WT"    "Mutant"
3    "prova05.txt"    "prova06.txt"    "WT"    "Mutant"

but readin in the limma user guide i'm not able to read the 6 chip

 > library("limma")
 > targets <- readTargets()
 > targets
   SlideNumber FileNameCy3 FileNameCy5 Cy3    Cy5
1           1 prova01.txt prova02.txt  WT Mutant
2           2 prova03.txt prova04.txt  WT Mutant
3           3 prova05.txt prova06.txt  WT Mutant
 > files <- targets[,c("FileNameCy3","FileNameCy5")]
 > files
   FileNameCy3 FileNameCy5
1 prova01.txt prova02.txt
2 prova03.txt prova04.txt
3 prova05.txt prova06.txt
 > RG <- read.maimages(files, source="imagene")
Read header information
Error in read.imagene(files = files, path = path, ext = ext, names = 
names,  :
   Can't find Field Dimensions in ImaGene header
In addition: Warning message:
In readImaGeneHeader(fullname) : End of file encountered before End Header

i know that "imagene" is not correct because i have used agilent 
Microarray Scanner (G2565CA) so i have the 6 txt files like the one that 
i have attached in the mail.

is there anyone that can help me in reading this kind of microarrays?

Best regards.

Alberto Goldoni, PhD
IT Lan Manager
Medical Genetics Unit
S. Orsola-Malpighi Hospital
Via Massarenti n.9, Pad 11
40100 Bologna, Italy

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