[BioC] imagene and limma

[Gordon Smyth]

Dear Servin,

You are mis-interpretting a little what the column names are intended 
to represent. They are names associated with the arrays, not with 
files or channels. All the data matrices (R, G, M and A) must share 
the same set of column names, because all relate to the same set of arrays.

When reading ImaGene data there isn't an obvious choice of array 
name, so the Cy3 file names are used. If you don't like this choice, 
you can use the 'names' argument of read.maimages().

Best wishes
Gordon

>Date: Wed, 29 Mar 2006 10:24:06 -0500
>From: "Sevin Turcan" <sevinturcan at gmail.com>
>Subject: [BioC] imagene and limma
>To: Bioconductor at stat.math.ethz.ch
>
>Dear list,
>
>I have a very basic question regarding reading imagene files. I have a
>targets.txt file as such:
>
>SlideNumber    FileNameCy3    FileNameCy5    Cy3    Cy5
>1    Cy3WT1.txt    Cy5KO1.txt    WT    Mu
>2    Cy3KO2.txt    Cy5WT2.txt    Mu    WT
>
>And when I try to read the file, everything seems to get read well except
>when I try to visualize the contents, the red channel columns are named
>Cy3WT1 and Cy3KO2 when they should be Cy5KO1 and Cy5WT2 (as I've pasted
>below). Any help would be appreciated. Thanks!
>
> > targets <- readTargets()
> > files <- targets[,c("FileNameCy3", "FileNameCy5")]
> > RG<-read.maimages(files, source="imagene")
>Read header information
>Read Cy3WT1.txt
>Read Cy5KO1.txt
>Read Cy3KO2.txt
>Read Cy5WT2.txt
> > show(RG)
>An object of class "RGList"
>$R
>          Cy3WT1    Cy3KO2
>[1,]   413.7954   404.293
>[2,] 31634.9648 48596.723
>[3,] 36108.0234 46955.476
>[4,]  7986.0908  6745.707
>[5,]  7147.1035 11792.948
>38875 more rows ...
>
>$G
>         Cy3WT1     Cy3KO2
>[1,]  1642.682   819.3275
>[2,] 33933.414 46091.7421
>[3,] 39531.910 43781.1132
>[4,]  8942.613  7269.6206
>[5,]  7607.328 12893.2929
>38875 more rows ...
>etc...