@@ -3159,9 +3159,13 @@ constructIlluminaAssayData <- function(np, snp, object, storage.mode="environmen

 			   CA=emptyMatrix,

 			   CB=emptyMatrix)

 }

-constructIlluminaCNSet <- function(res,

-				   cnAB,

-				   crlmmResult){

+constructIlluminaCNSet <- function(crlmmResult,

+				   snpFile,

+				   cnFile){

+	load(file.path(outdir, "snpFile.rda"))

+	res <- get("res")

+	load(file.path(outdir, "cnFile.rda"))

+	cnAB <- get("cnAB")	

 	fD <- constructIlluminaFeatureData(c(res$gns, cnAB$gns), cdfName="human370v1c")

 	new.order <- order(fD$chromosome, fD$position)

 	fD <- fD[new.order, ]

@@ -117,7 +117,7 @@ RG <- readIdatFiles2(samplesheet[1:10, ],

 		    arrayInfoColNames=list(barcode=NULL, position="SentrixPosition"), 

 		    saveDate=TRUE)

 annotation(RG) <- "human370v1c"

-crlmmResult <- crlmmIllumina(RG=RG, 

+crlmmResult <- crlmmIllumina2(RG=RG, 

 			     cdfName="human370v1c", 

 			     sns=pData(RG)$ID, 

 			     returnParams=TRUE,

@@ -127,20 +127,20 @@ crlmmResult <- crlmmIllumina(RG=RG,

 protocolData(crlmmResult)$ScanDate <- protocolData(RG)$ScanDate

 @ 

-\noindent Finally, we load a few of the intermediate files that were

-created during the preprocessing and genotyping.

-<<loadIntermediate, eval=FALSE>>=

-load(file.path(outdir, "snpFile.rda"))

-res <- get("res")

-load(file.path(outdir, "cnFile.rda"))

-cnAB <- get("cnAB")

-@ 

-

-<<loadIntermediate, echo=FALSE>>=

-trace(checkExists, browser)

-res <- checkExists("snpFile", .path=outdir, .FUN=load, file=file.path(outdir, "snpFile.rda"))

-cnAB <- checkExists("cnFile", .path=outdir, .FUN=load, file=file.path(outdir, "cnFile.rda"))

-@ 

+%\noindent Finally, we load a few of the intermediate files that were

+%created during the preprocessing and genotyping.

+%<<loadIntermediate, eval=FALSE>>=

+%load(file.path(outdir, "snpFile.rda"))

+%res <- get("res")

+%load(file.path(outdir, "cnFile.rda"))

+%cnAB <- get("cnAB")

+%@ 

+%

+%<<loadIntermediate, echo=FALSE>>=

+%trace(checkExists, browser)

+%res <- checkExists("snpFile", .path=outdir, .FUN=load, file=file.path(outdir, "snpFile.rda"))

+%cnAB <- checkExists("cnFile", .path=outdir, .FUN=load, file=file.path(outdir, "cnFile.rda"))

+%@ 

 After running the crlmm algorithm, we construct a container for

 storing the quantile normalized intensities, genotype calls, and

@@ -154,9 +154,9 @@ devel version of this package.

 container <- checkExists("container",

 			 .path=outdir,

 			 .FUN=constructIlluminaCNSet,

-			 res=res,

-			 cnAB=cnAB,

-			 crlmmResult=crlmmResult)

+			 crlmmResult=crlmmResult,

+			 snpFile=snpFile,

+			 cnFile=cnFile)

 @ 

 <<constructContainer2, eval=FALSE>>=