@@ -79,9 +79,9 @@ construct <- function(filenames, cdfName, copynumber=FALSE,

 	ffObjects <- list(alleleA=initializeBigMatrix(name="A", nr, nc),

 			  alleleB=initializeBigMatrix(name="B", nr, nc),

 			  call=initializeBigMatrix(name="call", nr, nc),

-			  callProbability=initializeBigMatrix(name="callPr", nr,nc),

-			  CA=initializeBigMatrix(name="CA", nr, nc),

-			  CB=initializeBigMatrix(name="CB", nr, nc))

+			  callProbability=initializeBigMatrix(name="callPr", nr,nc))

+##			  CA=initializeBigMatrix(name="CA", nr, nc),

+##			  CB=initializeBigMatrix(name="CB", nr, nc))

 	pd <- data.frame(matrix(NA, nc, 3), row.names=sns)

 	colnames(pd)=c("SKW", "SNR", "gender")

 	phenoData <- new("AnnotatedDataFrame", data=pd)

@@ -91,8 +91,8 @@ construct <- function(filenames, cdfName, copynumber=FALSE,

 		       alleleB=ffObjects[["alleleB"]],

 		       call=ffObjects[["call"]],

 		       callProbability=ffObjects[["callProbability"]],

-		       CA=ffObjects[["CA"]],

-		       CB=ffObjects[["CB"]],

+##		       CA=ffObjects[["CA"]],

+##		       CB=ffObjects[["CB"]],

 		       protocolData=protocolData,

 		       phenoData=phenoData,

 		       featureData=featureData,