@@ -47,7 +47,7 @@ getFeatureData <- function(cdfName, copynumber=FALSE){

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

 	}

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

-	M <- M[!is.na(M[, "chromosome"]), ]

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

 	M <- data.frame(M)

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

 }

@@ -163,8 +163,16 @@ if(!file.exists(file.path(outdir, "cnSet.rda"))){

 			     .FUN=genotype,

 			     filenames=celFiles,

 			     cdfName=cdfName,

-			     batch=batch, .load.it=FALSE)

-	class(calls(gtSet))

+			     batch=batch)

+	## try normalizing np probes on chr X

+	callSet <- gtSet

+	filenames <- celFiles

+	snp.I <- isSnp(callSet)

+	is.snp <- which(snp.I)

+	np.index <- which(!is.snp)

+

+

+

 }

 @

@@ -189,8 +197,7 @@ The \Rfunction{crlmmCopynumber} performs the following steps:

   displayed during the processing.

 <<LDS_copynumber>>=

-GT.CONF.THR <- 0.8

-cnSet <- checkExists("cnSet", .path=outdir, .FUN=crlmmCopynumber, object=gtSet, GT.CONF.THR=GT.CONF.THR)

+cnSet <- checkExists("cnSet", .path=outdir, .FUN=crlmmCopynumber, object=gtSet, .load.it=FALSE)

 @

 In an effort to reduce I/O, the \Rpackage{crlmmCopynumber} function no

@@ -219,7 +226,7 @@ the useful accessors for extracting which markers are SNPs, which are

 chromosomes, etc.

 <<ca>>=

-snp.index <- which(isSnp(cnSet) & chromosome(cnSet) < 23)

+snp.index <- which(isSnp(cnSet) & !is.na(chromosome(cnSet)))

 ca <- CA(cnSet, i=snp.index, j=1:5)

 cb <- CB(cnSet, i=snp.index, j=1:5)

 ct <- ca+cb

@@ -244,20 +251,22 @@ ct2 <- totalCopynumber(cnSet, i=marker.index, j=1:5)

 stopifnot(all.equal(ct, ct2))

 @

-  Nonpolymorphic markers on chromosome X:

-<<nonpolymorphicX, fig=TRUE, width=8, height=4>>=

-library(RColorBrewer)

-bp.cols <- brewer.pal(8, "Paired")[3:4]

+TODO: FIX estimation for nonpolymorphic markers on X

+

+<<nonpolymorphicX>>=

 npx.index <- which(chromosome(cnSet)==23 & !isSnp(cnSet))

+a <- A(cnSet)[npx.index, M]

+nus <- nuA(cnSet)[npx.index, ]

+## nu and phi are not estimated

 M <- sample(which(cnSet$gender==1), 5)

-cols <- bp.cols[cnSet$gender[c(M,F)]]

-cn.M <- CA(cnSet, i=npx.index, j=M)

-cn.F <- CA(cnSet, i=npx.index, j=F)

 F <- sample(which(cnSet$gender==2), 5)

-par(las=1)

-boxplot(data.frame(cbind(cn.M, cn.F)), pch=".", col=cols, outline=FALSE)

-legend("topleft", bty="n", fill=bp.cols, legend=c("male", "female"))

+X.markers <- which(!isSnp(cnSet) & chromosome(cnSet) == 23)

+cn.M <- CA(cnSet, i=X.markers, j=M)

+cn.F <- CA(cnSet, i=X.markers, j=F)

+##phi(cnSet, "A")[X.markers[1:10]]

+index <- which(is.na(nuA(cnSet)[X.markers, 1]))

+boxplot(data.frame(cbind(cn.M, cn.F)), pch=".")

 @

 \begin{figure}[t!]

@@ -1,3 +1,2 @@

-rsync -avuzb --exclude '*~' --exclude '.git*' -e ssh ~/madman/Rpacks/git/crlmm/ enigma2.jhsph.edu:~/madman/Rpacks/git/crlmm

-rsync -avuzb --exclude '*~' --exclude '.git*' -e ssh enigma2.jhsph.edu:~/madman/Rpacks/git/crlmm/inst/scripts/*opynumber.pdf ~/madman/Rpacks/git/crlmm/inst/scripts/

+rsync -avuzb --exclude '.git*' -e ssh ~/madman/Rpacks/git/crlmm/ enigma2.jhsph.edu:~/madman/Rpacks/release/crlmm