[BioC] imagene and limma

[Gordon Smyth]

I could change the default array names for Imagene source data to be

    paste(removeExt(FileNameCy3),removeExt(FileNameCy5))

instead of just

    removeExt(FileNameCy3)

Would that be preferable to ImaGene users?

Gordon


>To: "Sevin Turcan" <sevinturcan at gmail.com>
>From: Gordon Smyth <smyth at wehi.edu.au>
>Subject: [BioC] imagene and limma
>Cc: bioconductor at stat.math.ethz.ch
>
>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...