@@ -1251,20 +1251,17 @@ genotype.Illumina <- function(sampleSheet=NULL,

 			      recallRegMin=1000,

 			      gender=NULL,

 			      returnParams=TRUE,

-			      badSNP=0.7,

-			      callSet) {

+			      badSNP=0.7) {

 	is.lds = ifelse(isPackageLoaded("ff"), TRUE, FALSE)

 	stopifnot(is.lds)

 	if(missing(cdfName)) stop("must specify cdfName")

 	if(!isValidCdfName(cdfName)) stop("cdfName not valid.  see validCdfNames")

         pkgname = getCrlmmAnnotationName(cdfName)

-	if(missing(callSet) | !validObject(callSet)){

-		callSet <- construct.Illumina(sampleSheet=sampleSheet, arrayNames=arrayNames,

+	callSet <- construct.Illumina(sampleSheet=sampleSheet, arrayNames=arrayNames,

 				      ids=ids, path=path, arrayInfoColNames=arrayInfoColNames,

 				      highDensity=highDensity, sep=sep, fileExt=fileExt,

 				      cdfName=cdfName, copynumber=copynumber, verbose=verbose, batch=batch, # fns=fns,

 				      saveDate=saveDate) #, outdir=outdir)

-	}

 	## Basic checks

 	##check that mixtureParams provided

 	if(missing(mixtureParams))