[BioC] help on reading Agilent 44k 2 colour

[Yong Li]

Dear Alberto,

as you know your files are from Agilent scanner you should use
source="agilent" when calling read.maimages. Type ?read.maimages you
will see details of how to use that function.

A strange thing is that from your targets it seems you have one file
for Cy3 and another file for Cy5. I never see Agilent 2 colour txt
files like this. Normally one txt file for one chip, which includes
both the Cy3 and Cy5 data. You might want to check this.

Hope this helps.

Yong

On Wed, 17 Mar 2010 10:39:22 +0100
 Alberto Goldoni <alberto.goldoni at segesta.pro> wrote:
> 
> 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
> ----------------------------------------
>