@@ -30,7 +30,7 @@ readIdatFiles <- function(sampleSheet=NULL,

 			       barcode = sampleSheet[,arrayInfoColNames$barcode]

 			       arrayNames=barcode

 		       }

-		       if(!is.null(arrayInfoColNames$position) && (arrayInfoColNames$position %in% colnames(sampleSheet))) {  

+		       if(!is.null(arrayInfoColNames$position) && (arrayInfoColNames$position %in% colnames(sampleSheet))) {

 			       position = sampleSheet[,arrayInfoColNames$position]

 			       if(is.null(arrayNames))

 				       arrayNames=position

@@ -44,7 +44,7 @@ readIdatFiles <- function(sampleSheet=NULL,

 		       }

 	       }

 	       pd = new("AnnotatedDataFrame", data = sampleSheet)

-	       sampleNames(pd) <- basename(arrayNames)               

+	       sampleNames(pd) <- basename(arrayNames)

        }

        if(is.null(arrayNames)) {

                arrayNames = gsub(paste(sep, fileExt$green, sep=""), "", dir(pattern=fileExt$green, path=path))

@@ -54,7 +54,7 @@ readIdatFiles <- function(sampleSheet=NULL,

                }

                pd = new("AnnotatedDataFrame", data = data.frame(Sample_ID=arrayNames))

        }

-       

+

        narrays = length(arrayNames)

        grnfiles = paste(arrayNames, fileExt$green, sep=sep)

        redfiles = paste(arrayNames, fileExt$red, sep=sep)

@@ -71,7 +71,7 @@ readIdatFiles <- function(sampleSheet=NULL,

 	       redidats <- redfiles

        }

        if(!all(file.exists(grnidats))) stop("Missing some of the *Grn.idat files")

-       if(!all(file.exists(redidats))) stop("Missing some of the *Red.idat files")       

+       if(!all(file.exists(redidats))) stop("Missing some of the *Red.idat files")

 ##       if(!all(c(redfiles,grnfiles) %in% dir(path=path))){

 ##	       stop("Missing .idat files: red\n", paste(redfiles[!(redfiles %in% dir(path=path))], sep=" "), "\n green\n",

 ##		    paste(grnfiles[!(grnfiles %in% dir(path=path))], sep=" "))

@@ -146,12 +146,12 @@ readIdatFiles <- function(sampleSheet=NULL,

 	       }

 	       rm(G)

 	       gc()

-         

+

 	       cat(paste(sep, fileExt$red, sep=""), "\n")

 	       R = readIDAT(redidats[i])

 	       idsR = rownames(R$Quants)

-         

-	       if(length(ids)==length(idsG)) {   

+

+	       if(length(ids)==length(idsG)) {

 		       if(sum(ids==idsR)==nprobes) {

 			       RG@assayData$R[,i] = R$Quants[ ,"Mean"]

 				   zeroR = R$Quants[ ,"NBeads"]==0

@@ -204,7 +204,7 @@ readIdatFiles2 <- function(sampleSheet=NULL,

 			       barcode = sampleSheet[,arrayInfoColNames$barcode]

 			       arrayNames=barcode

 		       }

-		       if(!is.null(arrayInfoColNames$position) && (arrayInfoColNames$position %in% colnames(sampleSheet))) {  

+		       if(!is.null(arrayInfoColNames$position) && (arrayInfoColNames$position %in% colnames(sampleSheet))) {

 			       position = sampleSheet[,arrayInfoColNames$position]

 			       if(is.null(arrayNames))

 				       arrayNames=position

@@ -218,7 +218,7 @@ readIdatFiles2 <- function(sampleSheet=NULL,

 		       }

 	       }

 	       pd = new("AnnotatedDataFrame", data = sampleSheet)

-	       sampleNames(pd) <- basename(arrayNames)               

+	       sampleNames(pd) <- basename(arrayNames)

        }

        if(is.null(arrayNames)) {

                arrayNames = gsub(paste(sep, fileExt$green, sep=""), "", dir(pattern=fileExt$green, path=path))

@@ -228,7 +228,7 @@ readIdatFiles2 <- function(sampleSheet=NULL,

                }

                pd = new("AnnotatedDataFrame", data = data.frame(Sample_ID=arrayNames))

        }

-       

+

        narrays = length(arrayNames)

        grnfiles = paste(arrayNames, fileExt$green, sep=sep)

        redfiles = paste(arrayNames, fileExt$red, sep=sep)

@@ -245,7 +245,7 @@ readIdatFiles2 <- function(sampleSheet=NULL,

 	       redidats <- redfiles

        }

        if(!all(file.exists(grnidats))) stop("Missing some of the *Grn.idat files")

-       if(!all(file.exists(redidats))) stop("Missing some of the *Red.idat files")       

+       if(!all(file.exists(redidats))) stop("Missing some of the *Red.idat files")

 ##       if(!all(c(redfiles,grnfiles) %in% dir(path=path))){

 ##	       stop("Missing .idat files: red\n", paste(redfiles[!(redfiles %in% dir(path=path))], sep=" "), "\n green\n",

 ##		    paste(grnfiles[!(grnfiles %in% dir(path=path))], sep=" "))

@@ -327,12 +327,12 @@ readIdatFiles2 <- function(sampleSheet=NULL,

 	       }

 	       rm(G)

 	       gc()

-         

+

 	       cat(paste(sep, fileExt$red, sep=""), "\n")

 	       R = readIDAT(redidats[i])

 	       idsR = rownames(R$Quants)

-         

-	       if(length(ids)==length(idsG)) {   

+

+	       if(length(ids)==length(idsG)) {

 		       if(sum(ids==idsR)==nprobes) {

 			       RG@assayData$R[,i] = R$Quants[ ,"Mean"]

 		               zeroR = R$Quants[ ,"NBeads"]==0

@@ -369,24 +369,24 @@ readIDAT <- function(idatFile){

   }

-  versionNumber <- readBin(tempCon, "integer", n=1, size=8, 

+  versionNumber <- readBin(tempCon, "integer", n=1, size=8,

                            endian="little", signed=FALSE)

-  

-  nFields <- readBin(tempCon, "integer", n=1, size=4, 

+

+  nFields <- readBin(tempCon, "integer", n=1, size=4,

                      endian="little", signed=FALSE)

   fields <- matrix(0,nFields,3);

   colnames(fields) <- c("Field Code", "Byte Offset", "Bytes")

   for(i1 in 1:nFields){

-    fields[i1,"Field Code"] <- 

+    fields[i1,"Field Code"] <-

       readBin(tempCon, "integer", n=1, size=2, endian="little", signed=FALSE)

-    fields[i1,"Byte Offset"] <- 

+    fields[i1,"Byte Offset"] <-

       readBin(tempCon, "integer", n=1, size=8, endian="little", signed=FALSE)

   }

   knownCodes <- c(1000, 102, 103, 104, 107, 200, 300, 400,

                   401, 402, 403, 404, 405, 406, 407, 408, 409)

-  names(knownCodes) <- 

+  names(knownCodes) <-

     c("nSNPsRead",  # 1000

       "IlluminaID", #  102

       "SD",         #  103

@@ -419,35 +419,35 @@ readIDAT <- function(idatFile){

   }

   seek(tempCon, fields["nSNPsRead", "Byte Offset"])

-  nSNPsRead <- readBin(tempCon, "integer", n=1, size=4, 

+  nSNPsRead <- readBin(tempCon, "integer", n=1, size=4,

                        endian="little", signed=FALSE)

   seek(tempCon, fields["IlluminaID", "Byte Offset"])

-  IlluminaID <- readBin(tempCon, "integer", n=nSNPsRead, size=4, 

+  IlluminaID <- readBin(tempCon, "integer", n=nSNPsRead, size=4,

                        endian="little", signed=FALSE)

   seek(tempCon, fields["SD", "Byte Offset"])

-  SD <- readBin(tempCon, "integer", n=nSNPsRead, size=2, 

+  SD <- readBin(tempCon, "integer", n=nSNPsRead, size=2,

                 endian="little", signed=FALSE)

   seek(tempCon, fields["Mean", "Byte Offset"])

-  Mean <- readBin(tempCon, "integer", n=nSNPsRead, size=2, 

+  Mean <- readBin(tempCon, "integer", n=nSNPsRead, size=2,

                   endian="little", signed=FALSE)

   seek(tempCon, fields["NBeads", "Byte Offset"])

   NBeads <- readBin(tempCon, "integer", n=nSNPsRead, size=1, signed=FALSE)

   seek(tempCon, fields["MidBlock", "Byte Offset"])

-  nMidBlockEntries <- readBin(tempCon, "integer", n=1, size=4, 

+  nMidBlockEntries <- readBin(tempCon, "integer", n=1, size=4,

                               endian="little", signed=FALSE)

-  MidBlock <- readBin(tempCon, "integer", n=nMidBlockEntries, size=4, 

+  MidBlock <- readBin(tempCon, "integer", n=nMidBlockEntries, size=4,

                       endian="little", signed=FALSE)

   seek(tempCon, fields["RunInfo", "Byte Offset"])

-  nRunInfoBlocks <- readBin(tempCon, "integer", n=1, size=4, 

+  nRunInfoBlocks <- readBin(tempCon, "integer", n=1, size=4,

                             endian="little", signed=FALSE)

   RunInfo <- matrix(NA, nRunInfoBlocks, 5)

-  colnames(RunInfo) <- c("RunTime", "BlockType", "BlockPars", 

+  colnames(RunInfo) <- c("RunTime", "BlockType", "BlockPars",

                          "BlockCode", "CodeVersion")

   for(i1 in 1:2) { #nRunInfoBlocks){  ## MR edit

     for(i2 in 1:5){

@@ -457,50 +457,50 @@ readIDAT <- function(idatFile){

   }

   seek(tempCon, fields["RedGreen", "Byte Offset"])

-  RedGreen <- readBin(tempCon, "numeric", n=1, size=4, 

+  RedGreen <- readBin(tempCon, "numeric", n=1, size=4,

                       endian="little", signed=FALSE)

-  #RedGreen <- readBin(tempCon, "integer", n=4, size=1, 

+  #RedGreen <- readBin(tempCon, "integer", n=4, size=1,

   #                    endian="little", signed=FALSE)

   seek(tempCon, fields["MostlyNull", "Byte Offset"])

   nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE)

-  MostlyNull <- readChar(tempCon, nChars) 

+  MostlyNull <- readChar(tempCon, nChars)

   seek(tempCon, fields["Barcode", "Byte Offset"])

   nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE)

-  Barcode <- readChar(tempCon, nChars) 

+  Barcode <- readChar(tempCon, nChars)

   seek(tempCon, fields["ChipType", "Byte Offset"])

   nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE)

-  ChipType <- readChar(tempCon, nChars) 

+  ChipType <- readChar(tempCon, nChars)

   seek(tempCon, fields["MostlyA", "Byte Offset"])

   nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE)

-  MostlyA <- readChar(tempCon, nChars) 

+  MostlyA <- readChar(tempCon, nChars)

   seek(tempCon, fields["Unknown.1", "Byte Offset"])

   nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE)

-  Unknown.1 <- readChar(tempCon, nChars) 

+  Unknown.1 <- readChar(tempCon, nChars)

   seek(tempCon, fields["Unknown.2", "Byte Offset"])

   nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE)

-  Unknown.2 <- readChar(tempCon, nChars) 

+  Unknown.2 <- readChar(tempCon, nChars)

   seek(tempCon, fields["Unknown.3", "Byte Offset"])

   nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE)

-  Unknown.3 <- readChar(tempCon, nChars) 

+  Unknown.3 <- readChar(tempCon, nChars)

   seek(tempCon, fields["Unknown.4", "Byte Offset"])

   nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE)

-  Unknown.4 <- readChar(tempCon, nChars) 

+  Unknown.4 <- readChar(tempCon, nChars)

   seek(tempCon, fields["Unknown.5", "Byte Offset"])

   nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE)

-  Unknown.5 <- readChar(tempCon, nChars) 

+  Unknown.5 <- readChar(tempCon, nChars)

   close(tempCon)

-  Unknowns <- 

+  Unknowns <-

     list(MostlyNull=MostlyNull,

          MostlyA=MostlyA,

          Unknown.1=Unknown.1,

@@ -513,21 +513,21 @@ readIDAT <- function(idatFile){

   colnames(Quants) <- c("Mean", "SD", "NBeads")

   rownames(Quants) <- as.character(IlluminaID)

-  idatValues <- 

-    list(fileSize=fileSize, 

-         versionNumber=versionNumber, 

-         nFields=nFields, 

+  idatValues <-

+    list(fileSize=fileSize,

+         versionNumber=versionNumber,

+         nFields=nFields,

          fields=fields,

-         nSNPsRead=nSNPsRead, 

-         #IlluminaID=IlluminaID, 

-         #SD=SD, 

-         #Mean=Mean, 

+         nSNPsRead=nSNPsRead,

+         #IlluminaID=IlluminaID,

+         #SD=SD,

+         #Mean=Mean,

          #NBeads=NBeads,

          Quants=Quants,

-         MidBlock=MidBlock, 

-         RunInfo=RunInfo, 

-         RedGreen=RedGreen, 

-         Barcode=Barcode, 

+         MidBlock=MidBlock,

+         RunInfo=RunInfo,

+         RedGreen=RedGreen,

+         Barcode=Barcode,

          ChipType=ChipType,

          Unknowns=Unknowns)

@@ -538,20 +538,20 @@ readIDAT <- function(idatFile){

 readBPM <- function(bpmFile){

   ## Reads and parses Illumina BPM files

-  

+

   fileSize <- file.info(bpmFile)$size

   tempCon <- file(bpmFile,"rb")

   # The first few bytes of the egtFile are some type of

-  # header, but there's no related byte offset information. 

+  # header, but there's no related byte offset information.

   prefixCheck <- readChar(tempCon,3) ## should be "BPM"

   null.1 <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE)

-  ## should be 1  

-  

-  versionNumber <- 

+  ## should be 1

+

+  versionNumber <-

     readBin(tempCon, "integer", n=1, size=4, endian="little", signed=FALSE)

   ## should be 4

@@ -565,14 +565,14 @@ readBPM <- function(bpmFile){

   entriesByteOffset <- seek(tempCon);

   nEntries <- readBin(tempCon, "integer", n=1, size=4,

                       endian="little", signed=FALSE)

-    

+

   if(FALSE){

-    

+

     snpIndexByteOffset <- seek(tempCon)

     snpIndex <- readBin(tempCon, "integer", n=nEntries, size=4,

                         endian="little", signed=FALSE)

     ## for the 1M array, these are simply in order from 1 to 1072820.

-    

+

     snpNamesByteOffset <- seek(tempCon)

     snpNames <- rep("A", nEntries)

     for(i1 in 1:nEntries){

@@ -583,21 +583,21 @@ readBPM <- function(bpmFile){

   }

   seek(tempCon, 15278138)

-    

+

   normIDByteOffset <- seek(tempCon)

   normID <- readBin(tempCon, "integer", n=nEntries, size=1, signed=FALSE) + 1

-  

+

   newBlockByteOffset <- seek(tempCon)

   newBlock <- readBin(tempCon, "integer", n=10000, size=1, signed=FALSE)

-  

+

   close(tempCon)

   byteOffsets <- list(entriesByteOffset=entriesByteOffset,

-                      #snpIndexByteOffset=snpIndexByteOffset, 

+                      #snpIndexByteOffset=snpIndexByteOffset,

                       #snpNamesByteOffset=snpNamesByteOffset,

                       normIDByteOffset=normIDByteOffset,

                       newBlockByteOffset=newBlockByteOffset)

-  

+

   allStuff <- list(prefixCheck=prefixCheck,

                    null.1=null.1,

                    versionNumber=versionNumber,

@@ -611,7 +611,7 @@ readBPM <- function(bpmFile){

                    newBlock=newBlock,

                    byteOffsets=byteOffsets)

   allStuff

-  

+

 }

 RGtoXY = function(RG, chipType, verbose=TRUE) {

@@ -623,11 +623,12 @@ RGtoXY = function(RG, chipType, verbose=TRUE) {

                "human370quadv3c",        # 370CNV quad

                "human550v3b",            # 550K

                "human1mduov3b",          # 1M Duo

-               "humanomni1quadv1b")      # Omni1 quad

+               "humanomni1quadv1b",      # Omni1 quad

+	       "humanomniexpress12v1b")  # Omni express 12

   if(missing(chipType)){

 	  chipType = match.arg(annotation(RG), chipList)

   } else chipType = match.arg(chipType, chipList)

-  

+

   pkgname <- getCrlmmAnnotationName(chipType)

   if(!require(pkgname, character.only=TRUE, quietly=!verbose)){

      suggCall <- paste("library(", pkgname, ", lib.loc='/Altern/Lib/Loc')", sep="")

@@ -643,21 +644,21 @@ RGtoXY = function(RG, chipType, verbose=TRUE) {

   bids <- getVarInEnv("addressB") # comes from AddressB_ID or Address2 column in manifest

   ids <- names(aids)

   snpbase <- getVarInEnv("base")

-  

+

   nsnps = length(aids)

   narrays = ncol(RG)

-  

+

 #  aidcol = match("AddressA_ID", colnames(annot))

 #  if(is.na(aidcol))

 #    aidcol = match("Address", colnames(annot))

 #  bidcol = match("AddressB_ID", colnames(annot))

-#  if(is.na(bidcol)) 

+#  if(is.na(bidcol))

 #    bidcol = match("Address2", colnames(annot))

 #  aids = annot[, aidcol]

 #  bids = annot[, bidcol]

 #  snpids = annot[,"Name"]

-#  snpbase = annot[,"SNP"] 

-  infI = !is.na(bids) & bids!=0  

+#  snpbase = annot[,"SNP"]

+  infI = !is.na(bids) & bids!=0

   aord = match(aids, featureNames(RG)) # NAs are possible here

   bord = match(bids, featureNames(RG)) # and here

 #  argrg = aids[rrgg]

@@ -670,7 +671,7 @@ RGtoXY = function(RG, chipType, verbose=TRUE) {

                  annotation=chipType, phenoData=RG@phenoData, protocolData=RG@protocolData, storage.mode="environment")

   rm(tmpmat)

   gc()

-  

+

   # First sort out Infinium II SNPs, X -> R (allele A)  and Y -> G (allele B) from the same probe

   XY@assayData$X[!is.na(aord),] = exprs(channel(RG, "R"))[aord[!is.na(aord)],] # mostly red

   XY@assayData$Y[!is.na(aord),] = exprs(channel(RG, "G"))[aord[!is.na(aord)],] # mostly green

@@ -680,19 +681,19 @@ RGtoXY = function(RG, chipType, verbose=TRUE) {

 #  XY@assayData$Xse[!is.na(aord),] = exprs(channel(RG, "Rse"))[aord[!is.na(aord)],]

 #  XY@assayData$Yse[!is.na(aord),] = exprs(channel(RG, "Gse"))[aord[!is.na(aord)],]

   gc()

-  

+

   ## Warning - not 100% sure that the code below is correct - could be more complicated than this

-  

+

   # Next Infinium I where X -> R from allele A probe and Y -> R from allele B probe

 #  infIRR = infI & (snpbase=="[A/T]" | snpbase=="[T/A]" | snpbase=="[a/t]" | snpbase=="[t/a]")

-  

+

 #  X[infIRR,] = exprs(channel(RG, "R"))[aord[infIRR],] # mostly red

 #  Y[infIRR,] = exprs(channel(RG, "R"))[bord[infIRR],] # mostly green

 #  Xnb[infIRR,] = exprs(channel(RG, "Rnb"))[aord[infIRR],]

 #  Ynb[infIRR,] = exprs(channel(RG, "Rnb"))[bord[infIRR],]

 #  Xse[infIRR,] = exprs(channel(RG, "Rse"))[aord[infIRR],]

 #  Yse[infIRR,] = exprs(channel(RG, "Rse"))[bord[infIRR],]

-  

+

   # Finally Infinium I where X -> G from allele A probe and Y -> G from allele B probe

 #  infIGG = infI & (snpbase=="[C/G]" | snpbase=="[G/C]" | snpbase=="[g/c]" | snpbase=="[c/g]")

@@ -702,11 +703,11 @@ RGtoXY = function(RG, chipType, verbose=TRUE) {

 #  Ynb[infIGG,] = exprs(channel(RG, "Gnb"))[bord[infIGG],]

 #  Xse[infIGG,] = exprs(channel(RG, "Gse"))[aord[infIGG],]

 #  Yse[infIGG,] = exprs(channel(RG, "Gse"))[bord[infIGG],]

-    

+

   #  For now zero out Infinium I probes

   XY@assayData$X[infI,] = 0

   XY@assayData$Y[infI,] = 0

-  XY@assayData$zero[infI,] = 0  

+  XY@assayData$zero[infI,] = 0

 #  XY@assayData$Xnb[infI,] = 0

 #  XY@assayData$Ynb[infI,] = 0

 #  XY@assayData$Xse[infI,] = 0

@@ -721,7 +722,7 @@ RGtoXY = function(RG, chipType, verbose=TRUE) {

 RGtoXY2 = function(RG, chipType, verbose=TRUE) {

-  chipList = c("human1mv1c",             # 1M

+	  chipList = c("human1mv1c",             # 1M

                "human370v1c",            # 370CNV

                "human650v3a",            # 650Y

                "human610quadv1b",        # 610 quad

@@ -729,11 +730,12 @@ RGtoXY2 = function(RG, chipType, verbose=TRUE) {

                "human370quadv3c",        # 370CNV quad

                "human550v3b",            # 550K

                "human1mduov3b",          # 1M Duo

-               "humanomni1quadv1b")      # Omni1 quad

+               "humanomni1quadv1b",      # Omni1 quad

+	       "humanomniexpress12v1b")  # Omni express 12

   if(missing(chipType)){

 	  chipType = match.arg(annotation(RG), chipList)

   } else chipType = match.arg(chipType, chipList)

-  

+

   pkgname <- getCrlmmAnnotationName(chipType)

   if(!require(pkgname, character.only=TRUE, quietly=!verbose)){

      suggCall <- paste("library(", pkgname, ", lib.loc='/Altern/Lib/Loc')", sep="")

@@ -749,21 +751,21 @@ RGtoXY2 = function(RG, chipType, verbose=TRUE) {

   bids <- getVarInEnv("addressB") # comes from AddressB_ID or Address2 column in manifest

   ids <- names(aids)

   snpbase <- getVarInEnv("base")

-  

+

   nsnps = length(aids)

   narrays = ncol(RG)

-  

+

 #  aidcol = match("AddressA_ID", colnames(annot))

 #  if(is.na(aidcol))

 #    aidcol = match("Address", colnames(annot))

 #  bidcol = match("AddressB_ID", colnames(annot))

-#  if(is.na(bidcol)) 

+#  if(is.na(bidcol))

 #    bidcol = match("Address2", colnames(annot))

 #  aids = annot[, aidcol]

 #  bids = annot[, bidcol]

 #  snpids = annot[,"Name"]

-#  snpbase = annot[,"SNP"] 

-  infI = !is.na(bids) & bids!=0  

+#  snpbase = annot[,"SNP"]

+  infI = !is.na(bids) & bids!=0

   aord = match(aids, featureNames(RG)) # NAs are possible here

   bord = match(bids, featureNames(RG)) # and here

 #  argrg = aids[rrgg]

@@ -782,7 +784,7 @@ RGtoXY2 = function(RG, chipType, verbose=TRUE) {

   XY@assayData$X[1:nsnps,] = 0

   XY@assayData$Y[1:nsnps,] = 0

   XY@assayData$zero[1:nsnps,] = 0

-  

+

   # First sort out Infinium II SNPs, X -> R (allele A)  and Y -> G (allele B) from the same probe

   XY@assayData$X[!is.na(aord),] = exprs(channel(RG, "R"))[aord[!is.na(aord)],] # mostly red

   XY@assayData$Y[!is.na(aord),] = exprs(channel(RG, "G"))[aord[!is.na(aord)],] # mostly green

@@ -792,19 +794,19 @@ RGtoXY2 = function(RG, chipType, verbose=TRUE) {

 #  XY@assayData$Xse[!is.na(aord),] = exprs(channel(RG, "Rse"))[aord[!is.na(aord)],]

 #  XY@assayData$Yse[!is.na(aord),] = exprs(channel(RG, "Gse"))[aord[!is.na(aord)],]

   gc()

-  

+

   ## Warning - not 100% sure that the code below is correct - could be more complicated than this

-  

+

   # Next Infinium I where X -> R from allele A probe and Y -> R from allele B probe

 #  infIRR = infI & (snpbase=="[A/T]" | snpbase=="[T/A]" | snpbase=="[a/t]" | snpbase=="[t/a]")

-  

+

 #  X[infIRR,] = exprs(channel(RG, "R"))[aord[infIRR],] # mostly red

 #  Y[infIRR,] = exprs(channel(RG, "R"))[bord[infIRR],] # mostly green

 #  Xnb[infIRR,] = exprs(channel(RG, "Rnb"))[aord[infIRR],]

 #  Ynb[infIRR,] = exprs(channel(RG, "Rnb"))[bord[infIRR],]

 #  Xse[infIRR,] = exprs(channel(RG, "Rse"))[aord[infIRR],]

 #  Yse[infIRR,] = exprs(channel(RG, "Rse"))[bord[infIRR],]

-  

+

   # Finally Infinium I where X -> G from allele A probe and Y -> G from allele B probe

 #  infIGG = infI & (snpbase=="[C/G]" | snpbase=="[G/C]" | snpbase=="[g/c]" | snpbase=="[c/g]")

@@ -814,11 +816,11 @@ RGtoXY2 = function(RG, chipType, verbose=TRUE) {

 #  Ynb[infIGG,] = exprs(channel(RG, "Gnb"))[bord[infIGG],]

 #  Xse[infIGG,] = exprs(channel(RG, "Gse"))[aord[infIGG],]

 #  Yse[infIGG,] = exprs(channel(RG, "Gse"))[bord[infIGG],]

-    

+

   #  For now zero out Infinium I probes

   XY@assayData$X[infI,] = 0

   XY@assayData$Y[infI,] = 0

-  XY@assayData$zero[infI,] = 0  

+  XY@assayData$zero[infI,] = 0

 #  XY@assayData$Xnb[infI,] = 0

 #  XY@assayData$Ynb[infI,] = 0

 #  XY@assayData$Xse[infI,] = 0

@@ -846,10 +848,10 @@ stripNormalize = function(XY, useTarget=TRUE, verbose=TRUE) {

 #  data(preprocStuff, package=pkgname, envir=.crlmmPkgEnv)

   stripnum <- getVarInEnv("stripnum")

-  

+

   if(useTarget)

     targetdist = getVarInEnv("reference")

-  

+

 #  Xqws = Yqws = matrix(0, nrow(XY), ncol(XY))

 #  colnames(Xqws) = colnames(Yqws) = sampleNames(XY) #$X

 #  rownames(Xqws) = rownames(Yqws) = featureNames(XY)

@@ -857,7 +859,7 @@ stripNormalize = function(XY, useTarget=TRUE, verbose=TRUE) {

   if(verbose){

     message("Quantile normalizing ", ncol(XY), " arrays by ", max(stripnum), " strips.")

     if (getRversion() > '2.7.0') pb <- txtProgressBar(min=0, max=max(stripnum), style=3)

-  } 

+  }

   for(s in 1:max(stripnum)) {

     if(verbose) {

       if (getRversion() > '2.7.0') setTxtProgressBar(pb, s)

@@ -937,7 +939,7 @@ preprocessInfinium2 <- function(XY, mixtureSampleSize=10^5,

   SMEDIAN <- getVarInEnv("SMEDIAN")

   theKnots <- getVarInEnv("theKnots")

   gns <- getVarInEnv("gns")

-  

+

   # separate out copy number probes

   npIndex = getVarInEnv("npProbesFid")

   nprobes = length(npIndex)

@@ -946,24 +948,24 @@ preprocessInfinium2 <- function(XY, mixtureSampleSize=10^5,

   B <- matrix(as.integer(exprs(channel(XY, "Y"))[npIndex,]), nprobes, narrays)

   # new lines below - useful to keep track of zeroed out probes

-  zero <- matrix(as.integer(exprs(channel(XY, "zero"))[npIndex,]), nprobes, narrays) 

+  zero <- matrix(as.integer(exprs(channel(XY, "zero"))[npIndex,]), nprobes, narrays)

   colnames(A) <- colnames(B) <- colnames(zero) <- sns

   rownames(A) <- rownames(B) <- rownames(zero) <- names(npIndex)

-  

+

   cnAB = list(A=A, B=B, zero=zero, sns=sns, gns=names(npIndex), cdfName=cdfName)

   if(save.it & !missing(cnFile)) {

-    t0 <- proc.time() 

-    save(cnAB, file=cnFile) 

+    t0 <- proc.time()

+    save(cnAB, file=cnFile)

     t0 <- proc.time()-t0

     if(verbose) message("Used ", round(t0[3],1), " seconds to save ", cnFile, ".")

   }

   rm(cnAB, B, zero)

-  

+

   # next process snp probes

   snpIndex = getVarInEnv("snpProbesFid")

   nprobes <- length(snpIndex)

-  

+

   ##We will read each cel file, summarize, and run EM one by one

   ##We will save parameters of EM to use later

   mixtureParams <- matrix(0, 4, narrays)

@@ -977,7 +979,7 @@ preprocessInfinium2 <- function(XY, mixtureSampleSize=10^5,

   set.seed(seed)

   idx <- sort(sample(autosomeIndex, mixtureSampleSize))

   idx2 <- sample(nprobes, 10^5)

-  

+

   ##S will hold (A+B)/2 and M will hold A-B

   ##NOTE: We actually dont need to save S. Only for pics etc...

   ##f is the correction. we save to avoid recomputing

@@ -986,10 +988,10 @@ preprocessInfinium2 <- function(XY, mixtureSampleSize=10^5,

   # new lines below - useful to keep track of zeroed out SNPs

   zero <- matrix(as.integer(exprs(channel(XY, "zero"))[snpIndex,]), nprobes, narrays)

-    

+

   colnames(A) <- colnames(B) <- colnames(zero) <- sns

   rownames(A) <- rownames(B) <- rownames(zero) <- names(snpIndex) # gns # featureNames(XY)

-  

+

   if(verbose){

      message("Calibrating ", narrays, " arrays.")

      if (getRversion() > '2.7.0') pb <- txtProgressBar(min=0, max=narrays, style=3)

@@ -1022,8 +1024,8 @@ preprocessInfinium2 <- function(XY, mixtureSampleSize=10^5,

   res = list(A=A, B=B, zero=zero, sns=sns, gns=gns, SNR=SNR, SKW=SKW, mixtureParams=mixtureParams, cdfName=cdfName)

   if(save.it & !missing(snpFile)) {

-    t0 <- proc.time() 

-    save(res, file=snpFile) 

+    t0 <- proc.time()

+    save(res, file=snpFile)

     t0 <- proc.time()-t0

     if(verbose) message("Used ", round(t0[3],1), " seconds to save ", snpFile, ".")

   }

@@ -1076,7 +1078,7 @@ preprocessInfinium2v2 <- function(XY, mixtureSampleSize=10^5,

   theKnots <- getVarInEnv("theKnots")

 #  gns <- featureNames(XY) # getVarInEnv("gns") # needs to include np probes - gns is only for snps

   narrays = ncol(XY)

-  

+

   if(save.it & !missing(cnFile)) {

     # separate out copy number probes

     npIndex = getVarInEnv("npProbesFid")

@@ -1085,29 +1087,29 @@ preprocessInfinium2v2 <- function(XY, mixtureSampleSize=10^5,

     B <- matrix(as.integer(exprs(channel(XY, "Y"))[npIndex,]), nprobes, narrays)

     # new lines below - useful to keep track of zeroed out probes

-    zero <- matrix(as.integer(exprs(channel(XY, "zero"))[npIndex,]), nprobes, narrays) 

+    zero <- matrix(as.integer(exprs(channel(XY, "zero"))[npIndex,]), nprobes, narrays)

     colnames(A) <- colnames(B) <- colnames(zero) <- sns

     rownames(A) <- rownames(B) <- rownames(zero) <- names(npIndex)

-  

+

     cnAB = list(A=A, B=B, zero=zero, sns=sns, gns=names(npIndex), cdfName=cdfName)

-    

-    t0 <- proc.time() 

-    save(cnAB, file=cnFile) 

+

+    t0 <- proc.time()

+    save(cnAB, file=cnFile)

     t0 <- proc.time()-t0

     if(verbose) message("Used ", round(t0[3],1), " seconds to save ", cnFile, ".")

      rm(cnAB, B, zero)

   }

-  

+

   # next process snp probes

   snpIndex = getVarInEnv("snpProbesFid")

   nprobes <- length(snpIndex)

-  

+

   ##We will read each cel file, summarize, and run EM one by one

   ##We will save parameters of EM to use later

   mixtureParams <- initializeBigMatrix("crlmmMixt-", 4, narrays, "double")

   SNR <- initializeBigVector("crlmmSNR-", narrays, "double")

-  SKW <- initializeBigVector("crlmmSKW-", narrays, "double") 

+  SKW <- initializeBigVector("crlmmSKW-", narrays, "double")

 #  mixtureParams <- matrix(0, 4, narrays)

 #  SNR <- vector("numeric", narrays)

 #  SKW <- vector("numeric", narrays)

@@ -1119,7 +1121,7 @@ preprocessInfinium2v2 <- function(XY, mixtureSampleSize=10^5,

   set.seed(seed)

   idx <- sort(sample(autosomeIndex, mixtureSampleSize))

   idx2 <- sample(nprobes, 10^5)

-  

+

   ##S will hold (A+B)/2 and M will hold A-B

   ##NOTE: We actually dont need to save S. Only for pics etc...

   ##f is the correction. we save to avoid recomputing

@@ -1138,15 +1140,15 @@ preprocessInfinium2v2 <- function(XY, mixtureSampleSize=10^5,

 #  if(!is.integer(A)) {

 #     A = matrix(as.integer(A), nrow(A), ncol(A))

 #     B = matrix(as.integer(B), nrow(B), ncol(B))

-#  }  

-    

+#  }

+

 #  colnames(A) <- colnames(B) <- colnames(zero) <- sns

 #  rownames(A) <- rownames(B) <- rownames(zero) <- names(snpIndex) # gns # featureNames(XY)

   A <- initializeBigMatrix("crlmmA-", nprobes, narrays, "integer")

   B <- initializeBigMatrix("crlmmB-", nprobes, narrays, "integer")

   zero <- initializeBigMatrix("crlmmZero-", nprobes, narrays, "integer")

-  

+

   if(verbose){

      message("Calibrating ", narrays, " arrays.")

      if (getRversion() > '2.7.0') pb <- txtProgressBar(min=0, max=narrays, style=3)

@@ -1155,7 +1157,7 @@ preprocessInfinium2v2 <- function(XY, mixtureSampleSize=10^5,

   for(i in 1:narrays){

      A[,i] = exprs(channel(XY, "X"))[snpIndex,i]

      B[,i] = exprs(channel(XY, "Y"))[snpIndex,i]

-     zero[,i] = exprs(channel(XY, "zero"))[snpIndex,i] 

+     zero[,i] = exprs(channel(XY, "zero"))[snpIndex,i]

 #    SKW[i] = mean((A[snpIndex,i][idx2]-mean(A[snpIndex,i][idx2]))^3)/(sd(A[snpIndex,i][idx2])^3)

      SKW[i] = mean((A[idx2,i]-mean(A[idx2,i]))^3)/(sd(A[idx2,i])^3)

     if(fitMixture){

@@ -1184,8 +1186,8 @@ preprocessInfinium2v2 <- function(XY, mixtureSampleSize=10^5,

              mixtureParams=mixtureParams, cdfName=cdfName) # , snpIndex=snpIndex, npIndex=npIndex)

   if(save.it & !missing(snpFile)) {

-    t0 <- proc.time() 

-    save(res, file=snpFile) 

+    t0 <- proc.time()

+    save(res, file=snpFile)

     t0 <- proc.time()-t0

     if(verbose) message("Used ", round(t0[3],1), " seconds to save ", snpFile, ".")

   }

@@ -1224,7 +1226,7 @@ crlmmIllumina <- function(RG, XY, stripNorm=TRUE, useTarget=TRUE,

         stop("Both RG and XY specified - please use one or the other")

     }

     if (missing(sns)) sns <- sampleNames(XY) #$X

-    

+

     res = preprocessInfinium2(XY, mixtureSampleSize=mixtureSampleSize, fitMixture=TRUE, verbose=verbose,

                         seed=seed, eps=eps, cdfName=cdfName, sns=sns, stripNorm=stripNorm, useTarget=useTarget,

                         save.it=save.it, snpFile=snpFile, cnFile=cnFile)

@@ -1245,7 +1247,7 @@ crlmmIllumina <- function(RG, XY, stripNorm=TRUE, useTarget=TRUE,

                   recallRegMin=1000, SNRMin=SNRMin,

                   returnParams=returnParams, badSNP=badSNP,

                   verbose=verbose)

-  

+

   res2[["SNR"]] <- res[["SNR"]]

   res2[["SKW"]] <- res[["SKW"]]

   rm(res)

@@ -1279,7 +1281,7 @@ crlmmIllumina2 <- function(RG, XY, stripNorm=TRUE, useTarget=TRUE,

         stop("Both RG and XY specified - please use one or the other")

     }

     if (missing(sns)) sns <- sampleNames(XY) #$X

-    

+

     res = preprocessInfinium2v2(XY, mixtureSampleSize=mixtureSampleSize, fitMixture=TRUE, verbose=verbose,

                         seed=seed, eps=eps, cdfName=cdfName, sns=sns, stripNorm=stripNorm, useTarget=useTarget) #,

                       #  save.it=save.it, snpFile=snpFile, cnFile=cnFile)

@@ -1295,13 +1297,13 @@ crlmmIllumina2 <- function(RG, XY, stripNorm=TRUE, useTarget=TRUE,

 #                    alleleB=initializeBigMatrix(name="B", nr=nrow(res[[1]]), nc=length(sns)),

 #                    call=initializeBigMatrix(name="call", nr=nrow(res[[1]]), nc=length(sns)),

 #                    callProbability=initializeBigMatrix(name="callPr", nr=nrow(res[[1]]), nc=length(sns)),

-#  	            annotation=cdfName, protocolData=protD, phenoData=phenD, featureData=fD) 

+#  	            annotation=cdfName, protocolData=protD, phenoData=phenD, featureData=fD)

 #    sampleNames(callSet) <- sns

 #    featureNames(callSet) <- res[["gns"]]

 #    pData(callSet)$SKW <- rep(NA, length(sns))

 #    pData(callSet)$SNR <- rep(NA, length(sns))

 #    pData(callSet)$gender <- rep(NA, length(sns))

-					  

+

   }else{

       if(verbose) message("Loading ", snpFile, ".")

         obj <- load(snpFile)

@@ -1311,8 +1313,8 @@ crlmmIllumina2 <- function(RG, XY, stripNorm=TRUE, useTarget=TRUE,

   }

  #   rm(phenD, protD , fD)

-	

-#    snp.index <- res$snpIndex #match(res$gns, featureNames(callSet))                

+

+#    snp.index <- res$snpIndex #match(res$gns, featureNames(callSet))

 #    suppressWarnings(A(callSet) <- res[["A"]])

 #    suppressWarnings(B(callSet) <- res[["B"]])

 #    pData(callSet)$SKW <- res$SKW

@@ -1321,7 +1323,7 @@ crlmmIllumina2 <- function(RG, XY, stripNorm=TRUE, useTarget=TRUE,

 #    rm(res); gc()

   if(row.names) row.names=res$gns else row.names=NULL

   if(col.names) col.names=res$sns else col.names=NULL

-  

+

   res2 <- crlmmGT2(A=res[["A"]], #as.matrix(A(callSet)[snp.index,]), # j]),

                   B=res[["B"]], # as.matrix(B(callSet)[snp.index,]),  # j]),

                   SNR=res[["SNR"]], # callSet$SNR, # [j],

@@ -1338,7 +1340,7 @@ crlmmIllumina2 <- function(RG, XY, stripNorm=TRUE, useTarget=TRUE,

                   verbose=verbose,

                   returnParams=returnParams,

                   badSNP=badSNP)

-#    rm(res); gc()  

+#    rm(res); gc()

 #    suppressWarnings(snpCall(callSet)[snp.index, j] <- tmp[["calls"]])

 #    suppressWarnings(snpCallProbability(callSet)[snp.index, j] <- tmp[["confs"]])

 #    callSet$gender[j] <- tmp$gender

@@ -1355,8 +1357,8 @@ crlmmIllumina2 <- function(RG, XY, stripNorm=TRUE, useTarget=TRUE,

 }

-## MR: Below is a more memory efficient version of crlmmIllumina() which 

-## reads in the .idats and genotypes in the one function and removes objects 

+## MR: Below is a more memory efficient version of crlmmIllumina() which

+## reads in the .idats and genotypes in the one function and removes objects

 ## after they have been used

 crlmmIlluminaV2 = function(sampleSheet=NULL,

 			  arrayNames=NULL,

@@ -1371,7 +1373,7 @@ crlmmIlluminaV2 = function(sampleSheet=NULL,

 #                          rgFile,

 			  stripNorm=TRUE,

 			  useTarget=TRUE,

-          	          row.names=TRUE, 

+          	          row.names=TRUE,

 			  col.names=TRUE,

 			  probs=c(1/3, 1/3, 1/3), DF=6, SNRMin=5, gender=NULL,

                           seed=1, save.ab=FALSE, snpFile, cnFile,

@@ -1382,7 +1384,7 @@ crlmmIlluminaV2 = function(sampleSheet=NULL,

   if(missing(cdfName)) stop("must specify cdfName")

   if(!isValidCdfName(cdfName)) stop("cdfName not valid.  see validCdfNames")

 #  if(missing(sns)) sns <- basename(arrayNames)

-			  

+

 #  if (save.rg & missing(rgFile))

 #    stop("'rgFile' is missing, and you chose save.rg")

   if (save.ab & (missing(snpFile) | missing(cnFile)))

@@ -1437,7 +1439,7 @@ crlmmIlluminaV2 = function(sampleSheet=NULL,

 #    featureNames(callSet) <- res[["gns"]]

 #    pData(callSet)$SKW <- rep(NA, length(sns))

 #    pData(callSet)$SNR <- rep(NA, length(sns))

-#    pData(callSet)$gender <- rep(NA, length(sns))			

+#    pData(callSet)$gender <- rep(NA, length(sns))

 #	}

 #	pData(callSet)[j,] <- phenD

 #	pData(protocolData(callSet))[j,] <- protD

@@ -1445,7 +1447,7 @@ crlmmIlluminaV2 = function(sampleSheet=NULL,

 #	pData(protocolData(callSet)) <- protD

 #    rm(phenD, protD, fD)

-	

+

 #    if(k > 1 & nrow(res[[1]]) != nrow(callSet)){

         ##RS: I don't understand why the IDATS for the

         ##same platform potentially have different lengths

@@ -1453,7 +1455,7 @@ crlmmIlluminaV2 = function(sampleSheet=NULL,

 #        res[["B"]] <- res[["B"]][res$gns %in% featureNames(callSet), ]

 #    }

-#    snp.index <- res$snpIndex #match(res$gns, featureNames(callSet))                

+#    snp.index <- res$snpIndex #match(res$gns, featureNames(callSet))

 #    suppressWarnings(A(callSet)[, j] <- res[["A"]])

 #    suppressWarnings(B(callSet)[, j] <- res[["B"]])

 #    suppressWarnings(A(callSet) <- res[["A"]])

@@ -1465,7 +1467,7 @@ crlmmIlluminaV2 = function(sampleSheet=NULL,

 #    mixtureParams <- res$mixtureParams

 #    rm(res); gc()

   if(row.names) row.names=res$gns else row.names=NULL

-  if(col.names) col.names=res$sns else col.names=NULL    

+  if(col.names) col.names=res$sns else col.names=NULL

   res2 <- crlmmGT2(A=res[["A"]], #as.matrix(A(callSet)[snp.index,]), # j]),

                   B=res[["B"]], # as.matrix(B(callSet)[snp.index,]),  # j]),

                   SNR=res[["SNR"]], # callSet$SNR, # [j],

@@ -1482,7 +1484,7 @@ crlmmIlluminaV2 = function(sampleSheet=NULL,

                   verbose=verbose,

                   returnParams=returnParams,

                   badSNP=badSNP)

-#    rm(res); gc()  

+#    rm(res); gc()

 #    suppressWarnings(snpCall(callSet)[snp.index, j] <- tmp[["calls"]])

 #    suppressWarnings(snpCallProbability(callSet)[snp.index, j] <- tmp[["confs"]])

 #    callSet$gender[j] <- tmp$gender

@@ -165,8 +165,10 @@ validCdfNames <- function(){

 	  "human610quadv1b",

 	  "human660quadv1a",

 	  "human1mduov3b",

-	  "humanomni1quadv1b")

+	  "humanomni1quadv1b",

+          "humanomniexpress12v1b")

 }

+

 isValidCdfName <- function(cdfName){

 	chipList <- validCdfNames()

 	result <- cdfName %in% chipList	

@@ -24,18 +24,18 @@

 <<setup, echo=FALSE, results=hide>>=

 options(continue=" ", width=70)

-@ 

+@

 %\section{Estimating copy number}

 %At present, software for copy number estimation is provided only for the

-%Affymetrix 6.0 platform.  

+%Affymetrix 6.0 platform.