@@ -29,7 +29,7 @@ importClassesFrom(oligoClasses, SnpSuperSet, AlleleSet, CNSet)

 importMethodsFrom(oligoClasses, allele, calls, "calls<-", confs,

 		  "confs<-", cnConfidence, "cnConfidence<-", isSnp,

 		  chromosome, position, A, B,

-		  "A<-", "B<-", open, close, lM, "lM<-")

+		  "A<-", "B<-", open, close, lM, "lM<-", flags, "flags<-")

 importFrom(oligoClasses, chromosome2integer, celfileDate, list.celfiles,

            copyNumber, initializeBigMatrix, initializeBigVector)

@@ -761,7 +761,7 @@ crlmmCopynumberLD <- function(object,

 		 neededPkgs="crlmm")

 	return(object)

 }

-yycrlmmCopynumber2 <- crlmmCopynumberLD

+crlmmCopynumber2 <- crlmmCopynumberLD

 fit.lm1 <- function(idxBatch,

 		    snpBatches,