@@ -92,3 +92,7 @@ and crlmmIllumina() in crlmm-illumina.R)

 2009-04-03 B Carvalho - committed version 1.0.70

 ** Updated TODO and DESCRIPTION

+

+2009-04-04 R.Scharpf - committed version 1.0.71

+

+*  bug in oneBatch function for chromosome X.  added additional checks for missing values

@@ -1,7 +1,7 @@

 Package: crlmm

 Type: Package

 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for SNP 5.0 and 6.0 arrays.

-Version: 1.0.70

+Version: 1.0.71

 Date: 2008-12-30

 Author: Rafael A Irizarry, Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>

 Maintainer: Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>

@@ -6,6 +6,5 @@ importFrom(utils, data, packageDescription, setTxtProgressBar, txtProgressBar)

 importFrom(stats, coef, cov, dnorm, kmeans, lm, mad, median, quantile, sd)

 importFrom(genefilter, rowSds)

 importFrom(mvtnorm, dmvnorm)

-

 export("crlmm", "list.celfiles", "computeCopynumber", "cnrma", "celDates", "crlmmIllumina", "readIdatFiles", "snprma")

 exportMethods("calls", "confs")

@@ -333,7 +333,7 @@ computeCopynumber <- function(chrom,

 		envir[["steps"]] <- rep(FALSE, 4)

 	}

 	##will be updating these objects

-	message("Sufficient statistics")

+	if(verbose) message("Sufficient statistics")

 	if(missing(P)) P <- seq(along=uplate)

 	steps <- envir[["steps"]]

 	if(!steps[1]){

@@ -664,12 +664,14 @@ oneBatch <- function(plateIndex,

 	}

 	nobsA <- Ns[, p, "A"] > 10

 	nobsB <- Ns[, p, "B"] > 10

+	notMissing <- !(is.na(muA[, p, "A"]) | is.na(muA[, p, "B"]) | is.na(muB[, p, "A"]) | is.na(muB[, p, "B"]))

 	complete <- list()

-	complete[[1]] <- which(correct.orderA & correct.orderB & nobsA) ##be selective here

-	complete[[2]] <- which(correct.orderA & correct.orderB & nobsB) ##be selective here	

+	complete[[1]] <- which(correct.orderA & correct.orderB & nobsA & notMissing) ##be selective here

+	complete[[2]] <- which(correct.orderA & correct.orderB & nobsB & notMissing) ##be selective here	

 	size <- min(5000, length(complete[[1]]))

 	if(size == 5000) complete <- lapply(complete, function(x) sample(x, size))

 	if(CHR == 23){

+		index <- list()

 		index[[1]] <- which(Ns[, p, "A"] == 0)

 		index[[2]] <- which(Ns[, p, "B"] == 0)

 		cols <- 2:1

@@ -1310,3 +1312,4 @@ biasAdjNP <- function(plateIndex, envir, priorProb){

 	normalNP[normalNP == FALSE] <- NA

 	envir[["normalNP"]] <- normalNP

 }

+