@@ -620,13 +620,13 @@ summarizeXGenotypes <- function(marker.index,

 				    DF.PRIOR,

 				    gender="male", ...){

 	if(gender == "male"){

-		sample.index <- which(gender==1)

-	} else sample.index <- which(gender==2)

+		sample.index <- which(object$gender==1)

+	} else sample.index <- which(object$gender==2)

 	nr <- length(marker.index)

 	nc <- length(batchNames(object))

 ##	NN.Mlist <- imputed.medianA <- imputed.medianB <- shrink.madA <- shrink.madB <- vector("list", nc)

 	NN.Mlist <- medianA <- medianB <- shrink.madA <- shrink.madB <- vector("list", nc)

-	gender <- object$gender

+	##gender <- object$gender

 	GG <- as.matrix(calls(object)[marker.index, sample.index])

 	CP <- as.matrix(snpCallProbability(object)[marker.index, sample.index])

 	AA <- as.matrix(A(object)[marker.index, sample.index])

@@ -682,7 +682,7 @@ summarizeXGenotypes <- function(marker.index,

 			madB <- cbind(statsB.AA[, 2], ##statsB.AB[, 2],

 				      statsB.BB[, 2])

 			NN <- cbind(N.AA, N.BB)

-			rm(statsA.AA, statsA.BB, statsB.AA, statsB.AB, statsB.BB)

+			rm(statsA.AA, statsA.BB, statsB.AA, statsB.BB)

 		} else {

 			medianA[[k]] <- cbind(statsA.AA[, 1], statsA.AB[, 1],

 					      statsA.BB[, 1])

@@ -702,12 +702,11 @@ summarizeXGenotypes <- function(marker.index,

 		## SNPs that we'll use for imputing location/scale of unobserved genotypes

 		##---------------------------------------------------------------------------

 		index.complete <- indexComplete(NN, medianA[[k]], medianB[[k]], MIN.OBS)

-

 		##---------------------------------------------------------------------------

 		## Impute sufficient statistics for unobserved genotypes (plate-specific)

 		##---------------------------------------------------------------------------

 		if(gender=="male"){

-			res <- imputeCenterX(medianA[[k]], medianB[[k]], NN.M, index.complete, MIN.OBS)

+			res <- imputeCenterX(medianA[[k]], medianB[[k]], NN, index.complete, MIN.OBS)

 		} else {

 			unobservedAA <- NN[, 1] < MIN.OBS

 			unobservedAB <- NN[, 2] < MIN.OBS