[BioC] ImaGene - Data analysis

Karin Lemuth karin.lemuth at po.uni-stuttgart.de
Fri Oct 24 10:34:32 MEST 2003

Dear Marcello, dear all,

I had a look on the discussion about the ImaGene data analysis via
Limma. And it was very helpful for me, because I could transfer it to my
problem. But now I can't go on and I don't know why. Seems I missed
s.th. very important. Maybe my problem is also the header of the ImaGene
file. I use an very old version of ImaGene (3.0) and I use limma 1.1.18
and R 1.7.1..

And that's what I do and get:

> library(limma)
> ArrayData<-read.table("alle.txt",header=TRUE)
> ArrayData
  SlideNumber FileNamecy3 FileNamecy5
1          48   48cy3.txt   48cy5.txt
2          50   50cy3.txt   50cy5.txt
3          51   51cy3.txt   51cy5.txt
4          52   52cy3.txt   52cy5.txt
5          57   57cy3.txt   57cy5.txt
6          61   61cy3.txt   61cy5.txt
7          64   64cy3.txt   64cy5.txt
> slides<-cbind(ArrayData$FileNamecy3,ArrayData$FileNamecy5)
>  RG<-read.maimages(slides, source="imagene")
Error in grep(pattern, x, ignore.case, extended, value) :
        invalid argument

Maybe you can give ma an advise for how to go on. Would be great,


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