@@ -473,3 +473,7 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.

      (currently saving intermediate steps in crlmmIlluminaRS)

      removed cnOptions function and changed arguments to crlmmCopynumber

+2010-03-18 R.Scharpf committed version 1.5.38

+

+** a few updates to initializeBigMatrix

+** show, [ defined for CNSetLM

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

 Package: crlmm

 Type: Package

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

-Version: 1.5.37

+Version: 1.5.38

 Date: 2010-02-05

 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>

@@ -67,6 +67,9 @@ construct <- function(filenames, cdfName, copynumber=FALSE, sns, verbose=TRUE){

 			 callProbability=initializeBigMatrix(name="callPr", nr,nc),

 			 featureData=featureData,

 			 annotation=cdfName)

+	pd <- data.frame(matrix(NA, nc, 3), row.names=sns)

+	colnames(pd)=c("SKW", "SNR", "gender")

+	phenoData(callSet) <- new("AnnotatedDataFrame", data=pd)

 	protocolData(callSet) <- protocolData

 	sampleNames(callSet) <- sns

 	return(callSet)

@@ -1,9 +1,9 @@

-setMethod("show", "CNSet", function(object){

+setMethod("show", "CNSetLM", function(object){

 	callNextMethod(object)

 	cat("lM: ", length(lM(object)), " elements \n")

 	print(names(lM(object)))

 })

-setMethod("[", "CNSet", function(x, i, j, ..., drop=FALSE){

+setMethod("[", "CNSetLM", function(x, i, j, ..., drop=FALSE){

 	x <- callNextMethod(x, i, j, ..., drop=drop)

 	if(!missing(i)){

 		if(class(lM(x)) == "ffdf"){

@@ -16,9 +16,9 @@ setMethod("[", "CNSet", function(x, i, j, ..., drop=FALSE){

 })

 setGeneric("lM", function(object) standardGeneric("lM"))

 setGeneric("lM<-", function(object, value) standardGeneric("lM<-"))

-setMethod("lM", "CNSet", function(object) object@lM)

+setMethod("lM", "CNSetLM", function(object) object@lM)

 ##setMethod("linearModelParam", "AffymetrixCNSet", function(object) object@linearModelParam)

-setReplaceMethod("lM", c("CNSet", "list_or_ffdf"), function(object, value){

+setReplaceMethod("lM", c("CNSetLM", "list_or_ffdf"), function(object, value){

 	object@lM <- value

 	object

 })

@@ -211,36 +211,34 @@ initializeBigMatrix <- function(name, nr, nc, vmode="integer"){

 		if(prod(nr, nc) > 2^31){

 			##Need multiple matrices

 			## -- use ffdf

-			

 			## How many samples per ff object

 			S <- floor(2^31/nr - 1)

-

 			## How many ff objects

 			L <- ceiling(nc/S)

 			name <- paste(name, 1:L, sep="_")

-

-			results <- vector("list", L)

+			resultsff <- vector("list", L)

 			##resultsB <- vector("list", L)			

 			for(i in 1:(L-1)){  ## the Lth object may have fewer than nc columns

-				results[[i]] <- createFF(name=name[i],

-							 dim=c(nr, S),

-							 vmode=vmode)

+				resultsff[[i]] <- createFF(name=name[i],

+							   dim=c(nr, S),

+							   vmode=vmode)

 			}

 			##the Lth element

 			leftOver <- nc - ((L-1)*S)

-			results[[L]] <- createFF(name=name[L],

-						 dim=c(nr, leftOver),

-						 vmode=vmode)

-			resultsff <- do.call(ffdf, results)

+			resultsff[[L]] <- createFF(name=name[L],

+						   dim=c(nr, leftOver),

+						   vmode=vmode)

+			resultsff[[L]][,] <- NA

+			results <- do.call(ffdf, resultsff)

+			rm(resultsff); gc()

 			##dimnames(resultsff) <- dns

 		} else {

-			resultsff <- createFF(name=name,

-					      dim=c(nr, nc),

-					      vmode=vmode)

+			results <- createFF(name=name,

+					    dim=c(nr, nc),

+					    vmode=vmode)

 		}

-		resultsff[,] <- NA

-	}  else resultsff <- matrix(NA, nr, nc)

-	return(resultsff)

+	}  else results <- matrix(NA, nr, nc)

+	return(results)

 }

 setMethod("annotatedDataFrameFrom", "ff_matrix", Biobase:::annotatedDataFrameFromMatrix)

 setMethod("annotatedDataFrameFrom", "ffdf", Biobase:::annotatedDataFrameFromMatrix)