@@ -429,3 +429,7 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.

 - the batchSize argument will run the genotyping (crlmmGT) in batches to reduce the RAM.  The default is batches of size 1000.

 - The crlmm.Rd file contains an example with / without ff for Affymetrix data.

+

+2010-03-08 M. Ritchie committed version 1.5.31

+ * removed a few unnecessary lines of code from crlmm-illumina.R (zero not needed as argument for preprocessInfinium2() and storageMode should not be "lockedEnvironment" in RGtoXY()) 

+ * added "humanomni1quadv1b" to validCdfName() in utils.R

@@ -1,8 +1,8 @@

 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: 1.5.30

-Date: 2010-03-07

+Version: 1.5.31

+Date: 2010-03-08

 Author: Rafael A Irizarry, Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>

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

 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms

@@ -453,14 +453,14 @@ RGtoXY <- function(RG, chipType) {

 	## RS: this should be put elsewhere -- perhaps in utils.R

 	##  -- see validCdfNames() in utils.R.  are these consistent?

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

-		      "human370v1c",            # 370CNV

-		      "human650v3a",            # 650Y

-		      "human610quadv1b",        # 610 quad

-		      "human660quadv1a",        # 660 quad

-		      "human370quadv3c",        # 370CNV quad

-		      "human550v3b",            # 550K

-		      "human1mduov3b",          # 1M Duo

-		      "humanomni1quadv1b")      # Omni1 quad

+		          "human370v1c",            # 370CNV

+		          "human650v3a",            # 650Y

+		          "human610quadv1b",        # 610 quad

+		          "human660quadv1a",        # 660 quad

+		          "human370quadv3c",        # 370CNV quad

+		          "human550v3b",            # 550K

+		          "human1mduov3b",          # 1M Duo

+		          "humanomni1quadv1b")      # Omni1 quad

 	if(missing(chipType)){

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

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

@@ -570,7 +570,7 @@ RGtoXY <- function(RG, chipType) {

 	##  XY@assayData$zero[XY@assayData$X==0 | XY@assayData$Y==0] = 1

 	gc()

-	storageMode(XY) = "lockedEnvironment"

+	## storageMode(XY) = "lockedEnvironment"

 	return(XY)

 }

@@ -619,7 +619,7 @@ stripNormalize = function(XY, useTarget=TRUE, verbose=TRUE) {

 	}

 	if(verbose)

 		cat("\n")

-	XY

+	return(XY)

 	##  XYNorm = new("NChannelSet",

 	##                X=Xqws+16,

 	##                Y=Yqws+16,

@@ -645,7 +645,7 @@ stripNormalize = function(XY, useTarget=TRUE, verbose=TRUE) {

 ##				save.it=FALSE,

 ##				snpFile,

 ##				cnFile) {

-preprocessInfinium2 <- function(object, zero){  

+preprocessInfinium2 <- function(object) { ## , zero){  

 	storageMode(object) <- "environment"

 	ops <- crlmmOptions(object)

 	mixtureSampleSize <- ops$snprmaOpts[["mixtureSampleSize"]]

@@ -798,8 +798,8 @@ preprocessInfinium2 <- function(object, zero){

 ##	}

 	##RS: I don't think A and B were updated, so probably do not need to reassign

-	A(object) <- A

-	B(object) <- B

+##	A(object) <- A

+##	B(object) <- B

 	if (!fitMixture) SNR <- mixtureParams <- NA

 	sampleStats <- data.frame(SKW=SKW,

 				  SNR=SNR)

@@ -170,7 +170,8 @@ validCdfNames <- function(){

 	  "human650v3a",

 	  "human610quadv1b",

 	  "human660quadv1a",

-	  "human1mduov3b")

+	  "human1mduov3b",

+	  "humanomni1quadv1b")

 }

 isValidCdfName <- function(cdfName){