@@ -693,6 +693,12 @@ preprocessInfinium2 <- function(XY, mixtureSampleSize=10^5,

     close(mixtureParams)

     close(SNR)

 #  }  

+

+  open(res[["A"]])

+  open(res[["B"]])

+  open(res[["zero"]])

+  open(res[["SNR"]])

+  open(res[["mixtureParams"]])

   res = list(A=A, B=B,

              zero=zero, sns=sns, gns=names(snpIndex), SNR=SNR, SKW=SKW,

@@ -705,6 +711,12 @@ preprocessInfinium2 <- function(XY, mixtureSampleSize=10^5,

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

   }

+  close(res[["A"]])

+  close(res[["B"]])

+  close(res[["zero"]])

+  close(res[["SNR"]])

+  close(res[["mixtureParams"]])

+

   return(res)

 }

@@ -738,10 +750,6 @@ crlmmIllumina <- function(RG, XY, stripNorm=TRUE, useTarget=TRUE,

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

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

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

-    open(res[["A"]])  # this should perhaps go below }else{ below

-    open(res[["B"]])

-    open(res[["SNR"]])

-    open(res[["mixtureParams"]])    

 #    fD = featureData(XY)

 #    phenD = XY@phenoData

@@ -769,8 +777,13 @@ crlmmIllumina <- function(RG, XY, stripNorm=TRUE, useTarget=TRUE,

           stop("Object in ", snpFile, " seems to be invalid.")

   }

+    open(res[["A"]])

+    open(res[["B"]])

+    open(res[["SNR"]])

+    open(res[["mixtureParams"]])

+

 #    rm(phenD, protD , fD)

-	

+

 #    snp.index <- res$snpIndex #match(res$gns, featureNames(callSet))                

 #    suppressWarnings(A(callSet) <- res[["A"]])

 #    suppressWarnings(B(callSet) <- res[["B"]])

@@ -873,6 +886,11 @@ crlmmIlluminaV2 = function(sampleSheet=NULL,

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

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

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

+    open(res[["A"]])

+    open(res[["B"]])

+    open(res[["SNR"]])

+    open(res[["mixtureParams"]])

+						   

 #    fD = featureData(XY)

 #    phenD = XY@phenoData

 #    protD = XY@protocolData