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...
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...
