@@ -615,11 +615,19 @@ preprocessInfinium2 <- function(XY, mixtureSampleSize=10^5,

     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) 

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

+

+      close(XY@assayData$X)

+      close(XY@assayData$Y)

+      close(XY@assayData$zero)

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

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

@@ -665,6 +673,10 @@ preprocessInfinium2 <- function(XY, mixtureSampleSize=10^5,

      if (getRversion() > '2.7.0') pb <- txtProgressBar(min=0, max=narrays, style=3)

   }

+  open(XY@assayData$X)

+  open(XY@assayData$Y)

+  open(XY@assayData$zero)

+  

   for(i in 1:narrays){

      A[,i] = exprs(channel(XY, "X"))[snpIndex,i]

      B[,i] = exprs(channel(XY, "Y"))[snpIndex,i]

@@ -693,6 +705,10 @@ preprocessInfinium2 <- function(XY, mixtureSampleSize=10^5,

   if (!fitMixture) SNR <- mixtureParams <- NA

   ## gns comes from preprocStuff.rda

+  close(XY@assayData$X)

+  close(XY@assayData$Y)

+  close(XY@assayData$zero)  

+  

 #  if(class(A)[1]=="ff_matrix") {

     close(A)

     close(B)

@@ -892,7 +908,7 @@ crlmmIlluminaV2 = function(sampleSheet=NULL,

     if (missing(sns)) { sns = sampleNames(XY) #subsns = sampleNames(XY)

     } # else subsns = sns[j]

     res = preprocessInfinium2(XY, mixtureSampleSize=mixtureSampleSize, fitMixture=TRUE, verbose=verbose,

-                               seed=seed, eps=eps, cdfName=cdfName, sns=sns, stripNorm=stripNorm, useTarget=useTarget, #) # sns=subsns

+                               seed=seed, eps=eps, cdfName=cdfName, sns=sns, stripNorm=stripNorm, useTarget=useTarget,

                                save.it=save.it, snpFile=snpFile, cnFile=cnFile)

     open(res[["A"]])

     open(res[["B"]])