@@ -68,21 +68,26 @@ construct <- function(filenames, cdfName, copynumber=FALSE,

 	rownames(pData(protocolData)) <- sns

 	featureData <- getFeatureData.Affy(cdfName, copynumber=copynumber)

 	nr <- nrow(featureData); nc <- length(filenames)

+	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))

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

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

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

 	callSet <- new("CNSetLM", 

-		       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),

+		       alleleA=ffObjects[["alleleA"]],

+		       alleleB=ffObjects[["alleleB"]],

+		       call=ffObjects[["call"]],

+		       callProbability=ffObjects[["callProbability"]],

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

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

 		       protocolData=protocolData,

+		       phenoData=phenoData,

 		       featureData=featureData,

 		       annotation=cdfName)

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

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

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

-	rownames(pData(callSet)) <- NULL

-	phenoData(callSet)$sampleNames <- sns

 	return(callSet)

 }