@@ -472,12 +472,20 @@ RGtoXY = function(RG, chipType, verbose=TRUE) {

   XY@assayData$Y[1:nsnps,] = 0

   XY@assayData$zero[1:nsnps,] = 0

+  open(RG@assayData$R)

+  open(RG@assayData$G)

+  open(RG@assayData$zero)

+  

   # First sort out Infinium II SNPs, X -> R (allele A)  and Y -> G (allele B) from the same probe

   XY@assayData$X[!is.na(aord),] = exprs(channel(RG, "R"))[aord[!is.na(aord)],] # mostly red

   XY@assayData$Y[!is.na(aord),] = exprs(channel(RG, "G"))[aord[!is.na(aord)],] # mostly green

   XY@assayData$zero[!is.na(aord),] = exprs(channel(RG, "zero"))[aord[!is.na(aord)],] # mostly green

   gc()

+  close(RG@assayData$R)

+  close(RG@assayData$G)

+  close(RG@assayData$zero)

+  

   ## Warning - not 100% sure that the code below is correct - could be more complicated than this

   # Next Infinium I where X -> R from allele A probe and Y -> R from allele B probe