@@ -349,8 +349,8 @@ shrinkGenotypeSummaries <- function(strata, index.list, object, MIN.OBS, MIN.SAM

 	shrink.corrBB <- corrBB <- as.matrix(corrBB(object)[marker.index, ])

 	flags <- as.matrix(flags(object)[marker.index, ])

 	for(k in seq(along=batches)){

-		B <- batches[[k]]

-		this.batch <- unique(as.character(batch(object)[B]))

+		sample.index <- batches[[k]]

+		this.batch <- unique(as.character(batch(object)[sample.index]))

 		medianA[[k]] <- cbind(medianA.AA[, k], medianA.AB[, k], medianA.BB[, k])

 		medianB[[k]] <- cbind(medianB.AA[, k], medianB.AB[, k], medianB.BB[, k])

 		madA <- cbind(madA.AA[, k], madA.AB[, k], madA.BB[, k])

@@ -359,7 +359,6 @@ shrinkGenotypeSummaries <- function(strata, index.list, object, MIN.OBS, MIN.SAM

 		##RS: estimate DF.PRIOR

 		shrink.madA[[k]] <- shrink(madA, NN, DF.PRIOR)

 		shrink.madB[[k]] <- shrink(madB, NN, DF.PRIOR)

-

 		## an estimate of the background variance is the MAD

 		## of the log2(allele A) intensities among subjects with

 		## genotypes BB

@@ -1425,7 +1424,7 @@ summarizeNps <- function(strata, index.list, object, batchSize,

 			gender <- object$gender[sample.index]

 			sample.index <- sample.index[gender == 2]

 			if(length(sample.index) == 0) next()

-s		}

+		}

 		this.batch <- unique(as.character(batch(object)[sample.index]))

 		j <- match(this.batch, batchnames)

 		I.A <- AA[, sample.index]

@@ -1515,6 +1514,7 @@ summarizeSnps <- function(strata,

 		stats <- summaryStats(G.AA, A, FUNS=c("rowMedians", "rowMAD"))

 		medianA.AA(object)[index, k] <- stats[, 1]

 		madA.AA(object)[index, k] <- stats[, 2]

+

 		stats <- summaryStats(G.AB, A, FUNS=c("rowMedians", "rowMAD"))

 		medianA.AB(object)[index, k] <- stats[, 1]

 		madA.AB(object)[index, k] <- stats[, 2]

@@ -1531,7 +1531,7 @@ summarizeSnps <- function(strata,

 		medianB.AB(object)[index, k] <- stats[, 1]

 		madB.AB(object)[index, k] <- stats[, 2]

-		statsB.BB[[k]] <- summaryStats(G.BB, B, FUNS=c("rowMedians", "rowMAD"))

+		stats <- summaryStats(G.BB, B, FUNS=c("rowMedians", "rowMAD"))

 		medianB.BB(object)[index, k] <- stats[, 1]

 		madB.BB(object)[index, k] <- stats[, 2]