@@ -536,3 +536,6 @@ function (which expects ff objects and supports parallel processing)

 2010-07-25 M. Ritchie committed version 1.7.6

 ** fixed bug introduced in 1.7.4 by addition of tryCatch() into readIdatFiles().  Thanks to Nolwenn Le Meur for pointing this out.

+

+2010--7-28 M. Ritchie committed version 1.7.7

+** added omni express 12 as one of the chip options for Illumina.  Also added a check for copy number probes (this chip doesn't have any).

@@ -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: 1.7.6

-Date: 2010-07-25

+Version: 1.7.7

+Date: 2010-07-28

 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

@@ -632,7 +632,8 @@ 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)

@@ -738,7 +739,8 @@ 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)

@@ -950,25 +952,27 @@ preprocessInfinium2 <- function(XY, mixtureSampleSize=10^5,

   # separate out copy number probes

   npIndex = getVarInEnv("npProbesFid")

   nprobes = length(npIndex)

-  narrays = ncol(XY)

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

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

+  if(length(nprobes)>0) {

+    narrays = ncol(XY)

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

+    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) 

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

+    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)

+    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()-t0

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

+    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()-t0

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

+    }

+    rm(cnAB, B, zero)

   }

-  rm(cnAB, B, zero)

-  

+

   # next process snp probes

   snpIndex = getVarInEnv("snpProbesFid")

   nprobes <- length(snpIndex)

@@ -1090,22 +1094,24 @@ preprocessInfinium2v2 <- function(XY, mixtureSampleSize=10^5,

     # separate out copy number probes

     npIndex = getVarInEnv("npProbesFid")

     nprobes = length(npIndex)

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

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

+    if(length(nprobes)>0) {

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

+      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) 

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

+      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)

+      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)

+      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()-t0

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

-     rm(cnAB, B, zero)

+      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

@@ -165,7 +165,8 @@ validCdfNames <- function(){

 	  "human610quadv1b",

 	  "human660quadv1a",

 	  "human1mduov3b",

-	  "humanomni1quadv1b")

+	  "humanomni1quadv1b",

+          "humanomniexpress12v1b")

 }

 isValidCdfName <- function(cdfName){

 	chipList <- validCdfNames()