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? Thanks to all! Regards. Emanuele M

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 ) Gordon >Thanks to all! >Regards. > >Emanuele M