Hi All,
  I'm using the latest version of limma to analyse a set of 3 gpr files.
  The QC filter I have created is as follows
  >myfun <- function(x,threshold=55){
  + okred <- abs(x[,"% > B635+2SD"]) > threshold
  + okgreen <- abs(x[,"% > B532+2SD"]) > threshold
  + okflag <- abs(x[,"Flags"]) > 0
  + okRGN <- abs(x[,"Rgn R2 (635/532)"] ) > 0.6
  + as.numeric(okgreen || okred || okflag || okRGN)
  +}
  
  Onreading in the gpr files using
  
  >RG <- read.maimages(targets$FileName, source="genepix",wt.fun=myfun)
  I get the following error
  
  Error in "[.data.frame"(x, , "% > B635+2SD") : 
          undefined columns selected
  
  I checked the columns and they are present in my gpr file.
  
  Why am I getting this error and how do I go about correcting it
  
  -Ankit
  

		
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