@@ -1302,22 +1302,15 @@ ellipseCenters <- function(object, index, allele, batch, log.it=TRUE){

 shrinkSummary <- function(object,

-			  type=c("SNP", "X.SNP"), ##"X.snps", "X.nps"),

+			  type="SNP", 

 			  MIN.OBS=1,

 			  MIN.SAMPLES=10,

 			  DF.PRIOR=50,

 			  verbose=TRUE,

 			  marker.index,

 			  is.lds){

-	stopifnot(type[[1]] %in% c("SNP", "X.SNP"))

-	if(type[[1]] == "X.SNP"){

-		gender <- object$gender

-		if(sum(gender == 2) < 3) {

-			message("too few females to estimate within genotype summary statistics on CHR X")

-			return(object)

-		}

-		CHR.X <- TRUE

-	} else CHR.X <- FALSE

+	stopifnot(type[[1]] != "SNP")

+	CHR.X <- FALSE ## this is no longer needed

 	if(missing(marker.index)){

 		batch <- batch(object)

 		is.snp <- isSnp(object)

@@ -1641,7 +1634,6 @@ crlmmCopynumber <- function(object,

 		       X.NP="chromosome X nonpolymorphic markers")

 	}

 	if(verbose) message("Computing summary statistics of the genotype clusters for each batch")

-##	for(i in seq_along(type)){

 	for(i in c(1, 2, 4)){ ## do not do X.SNP.  Do this during fit.lm3

 		marker.type <- type[i]

 		if(verbose) message(paste("...", mylabel(marker.type)))

@@ -1659,17 +1651,13 @@ crlmmCopynumber <- function(object,

 					  is.lds=is.lds)

 	}

 	if(verbose) message("Imputing unobserved genotype medians and shrinking the variances (within-batch, across loci) ")##SNPs only

-##	for(i in c(1, 2, 4)){

-##		marker.type <- type[i]

-##		if(!marker.type %in% c("SNP", "X.SNP")) next()

-##		message(paste("...", mylabel(marker.type)))

 	marker.index <- whichMarkers("SNP", is.snp,

 				     is.autosome, is.annotated, is.X)

 	object <- shrinkSummary(object=object,

 				MIN.OBS=MIN.OBS,

 				MIN.SAMPLES=MIN.SAMPLES,

 				DF.PRIOR=DF.PRIOR,

-				type=marker.type,

+				type="SNP",

 				verbose=verbose,

 				marker.index=marker.index,

 				is.lds=is.lds)