@@ -63,7 +63,8 @@ getFeatureData <- function(cdfName, copynumber=FALSE){

 		M[index, "isSnp"] <- 0L

 	}

 	##A few of the snpProbes do not match -- I think it is chromosome Y.

-	M[is.na(M[, "chromosome"]), "isSnp"] <- 1L

+	if(any(is.na(M[, "chromosome"])))

+		M[is.na(M[, "chromosome"]), "isSnp"] <- 1L

 	M <- data.frame(M)

 	return(new("AnnotatedDataFrame", data=M))

 }

@@ -1383,9 +1384,6 @@ imputeCenterX <- function(muA, muB, Ns, index.complete, MIN.OBS){

 }

-

-

-

 ## constructors for Illumina platform

 constructIlluminaFeatureData <- function(gns, cdfName){

 	pkgname <- paste(cdfName, "Crlmm", sep="")

@@ -1406,6 +1404,8 @@ constructIlluminaFeatureData <- function(gns, cdfName){

 	    data=data.frame(mapping),

 	    varMetadata=data.frame(labelDescription=colnames(mapping)))

 }

+

+

 constructIlluminaAssayData <- function(np, snp, object, storage.mode="environment", nr){

 	stopifnot(identical(snp$gns, featureNames(object)))

 	gns <- c(featureNames(object), np$gns)

@@ -1669,7 +1669,8 @@ summarizeSnps <- function(strata,

 			  index.list,

 			  object,

 			  GT.CONF.THR,

-			  verbose, CHR.X, ...){

+			  verbose,

+			  CHR.X, ...){

 ##	if(is.lds) {

 ##		physical <- get("physical")

 ##		open(object)

@@ -2776,6 +2777,9 @@ calculateRTheta <- function(cnSet, genotype=c("AA", "AB", "BB"), batch.name){

 	x[x < 64] <- 64

 	y[y < 64] <- 64

 	theta[, "theta"] <- atan2(y, x)*2/pi

+	if(any(is.na(theta))){

+		stop("NA's in thetas.  Can not compute theta / R values for batches with fewer than 10 samples")

+	}

 	## so that 'R' is available for NP probes

 	y[is.na(y)] <- 0

 	theta[, "R"] <- x+y

@@ -540,11 +540,12 @@ setMethod("calculateRBaf", signature(object="CNSet"),

 	RTheta.ab <- calculateRTheta(object, "AB", batch.name)

 	RTheta.bb <- calculateRTheta(object, "BB", batch.name)

-	theta.aa <- matrix(RTheta.aa[, "theta"], nrow(object), ncol(object), byrow=FALSE)

-	theta.ab <- matrix(RTheta.ab[, "theta"], nrow(object), ncol(object), byrow=FALSE)

-	theta.bb <- matrix(RTheta.bb[, "theta"], nrow(object), ncol(object), byrow=FALSE)

-

 	J <- which(batch(object) == batch.name)

+

+	theta.aa <- matrix(RTheta.aa[, "theta"], nrow(object), length(J), byrow=FALSE)

+	theta.ab <- matrix(RTheta.ab[, "theta"], nrow(object), length(J), byrow=FALSE)

+	theta.bb <- matrix(RTheta.bb[, "theta"], nrow(object), length(J), byrow=FALSE)

+

 	a <- A(object)[, J, drop=FALSE]

 	b <- B(object)[, J, drop=FALSE] ## NA's for b where nonpolymorphic

 	dns <- dimnames(a)

@@ -74,7 +74,8 @@ pathToCels <- "/thumper/ctsa/snpmicroarray/hapmap/raw/affy/1m"

 if(getRversion() < "2.13.0"){

 	rpath <- getRversion()

 } else rpath <- "trunk"

-outdir <- paste("/amber1/archive/oncbb/rscharpf/crlmm_vignette/", rpath, sep="")

+##outdir <- paste("/amber1/archive/oncbb/rscharpf/crlmm_vignette/", rpath, sep="")

+outdir <- paste("/amber1/archive/oncbb/rscharpf/crlmm_vignette/", rpath, "/gw6v1.5/", sep="")

 dir.create(outdir, recursive=TRUE, showWarnings=FALSE)

 @