@@ -143,16 +143,40 @@ plate <- samplesheet$Plate

 table(plate)

 ## too few samples to run the plates as separate batches

 batch <- as.factor(rep("1", nrow(samplesheet)))

-container <- checkExists("container", .path=outdir,

-			 .FUN=crlmm:::genotype.Illumina,

-			 sampleSheet=samplesheet,

-			 path=dirname(arrayNames[1]),

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

-			 cdfName="human370v1c",

-			 batch=batch,

-			 .load.it=load.it)

-cnSet <- checkExists("cnSet", .path=outdir, .FUN=crlmmCopynumber, object=container, .load.it="FALSE",

-		     GT.CONF.THR=0.8)

+if(!exists("crlmmResult")){

+	if(!file.exists(file.path(outdir, "crlmmResult.rda"))){

+		RG <- readIdatFiles(samplesheet,

+				    path=dirname(arrayNames[1]),

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

+				    saveDate=TRUE)

+		crlmmResult <- crlmmIllumina(RG=RG,

+					     cdfName="human370v1c",

+					     sns=pData(RG)$ID,

+					     returnParams=TRUE,

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

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

+					     save.it=TRUE)

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

+		range(protocolData(crlmmResult)$ScanDate)

+		save(crlmmResult, file=file.path(outdir, "crlmmResult.rda"))

+		rm(RG); gc()

+	} else{

+		message("Loading previously saved file...")

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

+	}

+}

+##container <- checkExists("container", .path=outdir,

+##			 .FUN=crlmm:::genotype.Illumina,

+##			 sampleSheet=samplesheet,

+##			 path=dirname(arrayNames[1]),

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

+##			 cdfName="human370v1c",

+##			 batch=batch,

+##			 .load.it=load.it)

+##GT.CONF.THR <- 0.8

+##cnSet <- checkExists("cnSet", .path=outdir, .FUN=crlmmCopynumber, object=container, .load.it=load.it,

+##		     GT.CONF.THR=GT.CONF.THR)

+q("no")

 @

 The \Robject{cnSet} returned by the \Rfunction{crlmmCopynumber}