[BioC] Error with read.imagene

Gordon Smyth smyth at wehi.edu.au
Thu Jul 1 01:00:57 CEST 2004

The error message is telling you that you have specified a foreground 
column name that doesn't exist. Is it possible that you meant "Signal 
Median" instead of "Median Signal"? ImaGene files do not have a column by 
the name you gave


At 03:08 AM 1/07/2004, marchiem\@libero\.it wrote:
>Hi to all,
>I wanted to read in the files in the same order of the target file but I 
>can't read the files names from the target file because the function wants 
>a 2 columns matrix...
>so that I created the matrix:
> > oxyfiles<-cbind(Oxytarget$FileNameCy3,Oxytarget$FileNameCy5)
>Now I have a matrix with the files in the same order of the target files 
>but when I try to read in the data I get this message:
> > RGo<-read.imagene(oxyfiles,columns=list(f="Median Signal",b="Background 
> Median"),names=Oxytarget$Name,path="C:/Program Files/R/rw1081/bin/oxyR")
>Read header information
>Read C:/Program Files/R/rw1081/bin/oxyR/2-4-04_SC19.57_Cy3_g58.txt
>Error in "[.data.frame"(obj, , columns$f) :
>         undefined columns selected
>Please can somebody tell me what I'm doing wrong? I find inconvenient use 
>the command dir(pattern=*.txt) to create the file with the arrays because 
>it stores them randomly...
>Thank you very much in advance.
>best regards.

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