@@ -548,3 +548,7 @@ function (which expects ff objects and supports parallel processing)

 ** Exported crlmmIlluminaV2(), which combines reading in of idats and genotyping in one.  Also added a man page for this function

 ** Added close() statements to readIdatFiles(), RGtoXY() and stripNormalize().  Added open() statement to stripNormalize(). Moved close() statement in preprocessInfinium2()

 ** tidied up crlmm-illumina.R, removing commented out code.

+

+2010-09-16 M. Ritchie 1.7.13

+** added immuno chip 12 as one of the chip options for Illumina.

+

@@ -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: 1.7.13

-Date: 2010-08-30

+Version: 1.7.14

+Date: 2010-09-16

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

 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

@@ -40,4 +40,3 @@ Collate: AllGenerics.R

          zzz.R

 LazyLoad: yes

 biocViews: Microarray, Preprocessing, SNP, Bioinformatics, CopyNumberVariants

-

@@ -419,7 +419,8 @@ RGtoXY = function(RG, chipType, verbose=TRUE) {

                "human550v3b",            # 550K

                "human1mduov3b",          # 1M Duo

                "humanomni1quadv1b",      # Omni1 quad

-	       "humanomniexpress12v1b")  # Omni express 12

+	       "humanomniexpress12v1b",  # Omni express 12

+               "humanimmuno12v1b")       # Immuno chip 12

   if(missing(chipType)){

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

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

@@ -167,7 +167,8 @@ validCdfNames <- function(){

 	  "human660quadv1a",

 	  "human1mduov3b",

 	  "humanomni1quadv1b",

-          "humanomniexpress12v1b")

+          "humanomniexpress12v1b",

+          "humanimmuno12v1b")

 }

 isValidCdfName <- function(cdfName){

 	chipList <- validCdfNames()