[BioC] imagene output

Gordon Smyth smyth at wehi.edu.au
Thu Dec 18 02:11:32 MET 2003

At 11:57 PM 17/12/2003, marchiem\@libero\.it wrote:
>Hi everybody,
>I have tried to read in output files from Imagene to limma:
> > files<-dir(pattern=".txt",path="E:/Lividans 1326 wt 16h vs DNA 
> B2/Lividans 1326 wt 16h vs DNA B2 data")
> > files
>[1] "SC8.3-19_Cy3_g52.txt" "SC8.3-19_Cy5_g37.txt"
> >RG<-read.maimages(files,source="imagene")
>But I receive the following message:
>Error in read.imagene(files = files, path = path, ext = ext, names = 
>names,  :
>         Need a two column matrix of file names
>Should I modify the .txt output files?and how?

As the help document says, and as the error message reminds you, you need a 
2-column matrix of file names. This is because Imagene, unlike other image 
analysis programs, makes separate files for the Cy3 and Cy5 channels and 
limma needs a way to tell which is which.

dim(files) <- c(1,2)
RG <- read.maimages(files, source="imagene", path= etc )


>Thanks to all!
>Emanuele M

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