@@ -957,25 +957,20 @@ fit.lm1 <- function(idxBatch,

 			phiA[phiA[, J] < MIN.PHI, J] <- MIN.PHI

 			phiB[phiB[, J] < MIN.PHI, J] <- MIN.PHI

 		}

-		## formerly polymorphic():  calculate copy number

-		cA[, k] <- matrix((1/phiA[, J]*(A-nuA[, J])), nrow(A), ncol(A))

-		cB[, k] <- matrix((1/phiB[, J]*(B-nuB[, J])), nrow(B), ncol(B))

+##		cA[, k] <- matrix((1/phiA[, J]*(A-nuA[, J])), nrow(A), ncol(A))

+##		cB[, k] <- matrix((1/phiB[, J]*(B-nuB[, J])), nrow(B), ncol(B))

 		rm(G, A, B, NORM, wA, wB, YA,YB, res, negA, negB, Np, Ns)

 		gc()

 	}

-	cA[cA < 0.05] <- 0.05

-	cB[cB < 0.05] <- 0.05

-	cA[cA > 5] <-  5

-	cB[cB > 5] <- 5

-	cA <- matrix(as.integer(cA*100), nrow(cA), ncol(cA))

-	cB <- matrix(as.integer(cB*100), nrow(cB), ncol(cB))

+##	cA[cA < 0.05] <- 0.05

+##	cB[cB < 0.05] <- 0.05

+##	cA[cA > 5] <-  5

+##	cB[cB > 5] <- 5

+##	cA <- matrix(as.integer(cA*100), nrow(cA), ncol(cA))

+##	cB <- matrix(as.integer(cB*100), nrow(cB), ncol(cB))

+##	CA(object)[snps, ] <- cA

+##	CB(object)[snps, ] <- cB

-

-	

-	CA(object)[snps, ] <- cA

-	CB(object)[snps, ] <- cB

-

-	

 	snpflags[snps, ] <- flags

 	lapply(lM(object), open)

@@ -2,7 +2,6 @@

 all:	illumina_copynumber copynumber 

 copynumber:	copynumber.Rnw

-##	echo "Sweave(\"$1.Rnw\"); library(tools); texi2dvi(\"$1.tex\", pdf=TRUE)" | R --no-save --no-restore;

 	echo "Stangle(\"copynumber.Rnw\")" | R --no-save --no-restore;	

 	cat ~/bin/cluster.template | perl -pe "s/Rprog/copynumber.R/" > copynumber.R.sh

 	qsub -m e -r y -cwd -l mem_free=12G,h_vmem=16G copynumber.R.sh

@@ -129,6 +129,7 @@ if(!file.exists(file.path(outdir, "cnSet.rda"))){

 					   batch=batch[1:20])

 	class(calls(gtSet.assayData_matrix))

 }

+q("no")

 @ 

 Next, we estimate copy number for the 20 CEL files.  The copy number

@@ -140,11 +141,6 @@ will load \Robject{cnSet.assayData_matrix} from disk if this

 computation had already been performed as part of the batch job.

 <<copynumber>>=

-stop()

-tms1 <- system.time(tmp <- crlmmCopynumber(gtSet.assayData_matrix))

-reload_pkg("crlmm")

-trace(nuphiAllele, browser)

-tms2 <- system.time(tmp <- crlmmCopynumber(gtSet.assayData_matrix))

 cnSet.assayData_matrix <- checkExists("cnSet.assayData_matrix",

 				      .path=outdir,

 				      .FUN=crlmmCopynumber,