@@ -939,28 +939,35 @@ preprocessInfinium2 <- function(XY, mixtureSampleSize=10^5,

   SMEDIAN <- getVarInEnv("SMEDIAN")

   theKnots <- getVarInEnv("theKnots")

   gns <- getVarInEnv("gns")

-

-  # separate out copy number probes

-  npIndex = getVarInEnv("npProbesFid")

-  nprobes = length(npIndex)

   narrays = ncol(XY)

-  A <- matrix(as.integer(exprs(channel(XY, "X"))[npIndex,]), nprobes, narrays)

-  B <- matrix(as.integer(exprs(channel(XY, "Y"))[npIndex,]), nprobes, narrays)

-

-  # new lines below - useful to keep track of zeroed out probes

-  zero <- matrix(as.integer(exprs(channel(XY, "zero"))[npIndex,]), nprobes, narrays)

-

-  colnames(A) <- colnames(B) <- colnames(zero) <- sns

-  rownames(A) <- rownames(B) <- rownames(zero) <- names(npIndex)

-  cnAB = list(A=A, B=B, zero=zero, sns=sns, gns=names(npIndex), cdfName=cdfName)

   if(save.it & !missing(cnFile)) {

-    t0 <- proc.time()

-    save(cnAB, file=cnFile)

-    t0 <- proc.time()-t0

-    if(verbose) message("Used ", round(t0[3],1), " seconds to save ", cnFile, ".")

+	  ## separate out copy number probes

+	  npIndex = getVarInEnv("npProbesFid")

+	  nprobes = length(npIndex)

+	  if(length(nprobes > 0)){

+		  open(XY@assayData$X)

+		  open(XY@assayData$Y)

+		  open(XY@assayData$zero)

+

+		  A <- matrix(as.integer(exprs(channel(XY, "X"))[npIndex,]), nprobes, narrays)

+		  B <- matrix(as.integer(exprs(channel(XY, "Y"))[npIndex,]), nprobes, narrays)

+

+		  ## new lines below - useful to keep track of zeroed out probes

+		  zero <- matrix(as.integer(exprs(channel(XY, "zero"))[npIndex,]), nprobes, narrays)

+

+		  colnames(A) <- colnames(B) <- colnames(zero) <- sns

+		  rownames(A) <- rownames(B) <- rownames(zero) <- names(npIndex)

+

+		  cnAB = list(A=A, B=B, zero=zero, sns=sns, gns=names(npIndex), cdfName=cdfName)

+

+		  t0 <- proc.time()

+		  save(cnAB, file=cnFile)

+		  t0 <- proc.time()-t0

+		  if(verbose) message("Used ", round(t0[3],1), " seconds to save ", cnFile, ".")

+		  rm(cnAB, B, zero)

+	  }

   }

-  rm(cnAB, B, zero)

   # next process snp probes

   snpIndex = getVarInEnv("snpProbesFid")