@@ -1,8 +1,7 @@

 \name{NEWS}

 \title{News for Package 'crlmm'}

-

-\section{Changes in version 1.9}{

+\section{Changes in version 1.10}{

   \subsection{USER VISIBLE CHANGES}{

     \itemize{

       \item Using NEWS.Rd

@@ -37,6 +37,27 @@

   }

 }

+\section{Changes in version 1.8}{

+  \subsection{USER VISIBLE CHANGES}{

+    \itemize{

+

+      \item define CNSet class with batch and batchStatistics slots

+

+      \item deprecate CNSetList class

+

+      \item deprecate crlmmWrapper, genotype2, and crlmmCopynumber2.

+      Use crlmmCopynumber in place of crlmmWrapper and crlmmCopynumber2.

+      Use genotype instead of genotype2.

+

+      \item raw copy number estimates no longer stored in container.  CA

+      and CB methods are no longer simple accessors to data stored in

+      the eset-extension.  These functions compute raw copy number

+      estimates from the linear model parameters.

+

+    }

+  }

+}

+

 \section{Changes in version 1.3}{

   \subsection{USER VISIBLE CHANGES}{

     \itemize{

@@ -16,15 +16,19 @@

       \item We have added several vignettes pertaining to copy number

       analyses in the crlmm package: CopyNumberOverview,

       AffymetrixPreprocessCN, IlluminaPreprocessCN, and Infrastructure.

+      The AffymetrixPreprocessCN and IlluminaPreprocessCN vignettes

+      provide instructions for preprocessing and genotyping the raw

+      intensities for Affymetrix and Illumina platforms, respectively.

       The 'copynumber' and 'Infrastructure' vignettes are applicable to

       both the Illumina and Affymetrix platforms. The CopyNumberOverview

-      vignette gives a brief summary of the available vignettes for copy

-      number analyses.

+      vignette provides a brief summary of the available vignettes for

+      copy number analysis.

-      \item Exporting function constructInf, preprocessInf, and

-      genotypeInf for preprocessing and genotyping Illumina files prior

-      to copy number analyses.  The genotype.Illumina function is now a

-      wrapper for these functions.

+      \item For those interested in copy number analysis of Illumina

+      platforms, we added functions that break-down the preprocessing

+      and genotyping steps: constructInf, preprocessInf, and

+      genotypeInf. The genotype.Illumina function is now a wrapper for

+      these functions.

       \item additional documentation for crlmm is provided in a

       compendium: http://www.biostat.jhsph.edu/~rscharpf/crlmmCompendium/index.html

@@ -1,10 +1,34 @@

 \name{NEWS}

 \title{News for Package 'crlmm'}

-\section{Changes in version 1.10}{

+

+\section{Changes in version 1.9}{

   \subsection{USER VISIBLE CHANGES}{

     \itemize{

       \item Using NEWS.Rd

+

+      \item batch slot in CNSet objects is class 'character'

+      (previously, class was 'factor')

+

+      \item the ff package is required for preprocessing and genotyping

+      prior to copy number analyses with the crlmmCopynumber function.

+

+      \item We have added several vignettes pertaining to copy number

+      analyses in the crlmm package: CopyNumberOverview,

+      AffymetrixPreprocessCN, IlluminaPreprocessCN, and Infrastructure.

+      The 'copynumber' and 'Infrastructure' vignettes are applicable to

+      both the Illumina and Affymetrix platforms. The CopyNumberOverview

+      vignette gives a brief summary of the available vignettes for copy

+      number analyses.

+

+      \item Exporting function constructInf, preprocessInf, and

+      genotypeInf for preprocessing and genotyping Illumina files prior

+      to copy number analyses.  The genotype.Illumina function is now a

+      wrapper for these functions.

+

+      \item additional documentation for crlmm is provided in a

+      compendium: http://www.biostat.jhsph.edu/~rscharpf/crlmmCompendium/index.html

+

     }

   }

 }

@@ -37,7 +61,7 @@

  	  elements of this object, including featureNames,

  	  sampleNames, and '['.

 	}

-	

+

         \item 'CopyNumberSet': contains locus-level estimates of copy

   	number for SNPs and polymorphic probes.

 	\enumerate{

@@ -47,7 +71,7 @@

 	  \item For nonpolymorphic probes, the total copy number is

           stored in the 'CA' slot and a NA is recorded for the

-          corresponding row in the CB matrix. 

+          corresponding row in the CB matrix.

 	  \item Useful methods: 'copyNumber', 'ellipse', 'points'

 	}

@@ -60,4 +84,5 @@

      'CrlmmSetList' and returns an object of class 'CopyNumberSet'.

     }

   }

+

 }

new file mode 100644

@@ -0,0 +1,63 @@

+\name{NEWS}

+\title{News for Package 'crlmm'}

+

+\section{Changes in version 1.10}{

+  \subsection{USER VISIBLE CHANGES}{

+    \itemize{

+      \item Using NEWS.Rd

+    }

+  }

+}

+

+\section{Changes in version 1.3}{

+  \subsection{USER VISIBLE CHANGES}{

+    \itemize{

+      \item 3 new classes created:

+      \itemize{

+	\item 'ABset': container for quantile-normalized A and B

+       	intensities for both SNP and copy number probes.  Required

+       	assay data elements are 'A' and 'B'.  Extends eSet

+       	directly.

+	\enumerate{

+          \item For nonpolymorphic probes, the quantile normalized

+          intensity is stored in the 'A' assay data element.

+          The corresponding row in the 'B' assay data element

+          is NA.  This is a bit inefficient, but greatly

+          simplifies downstream analyses.  In particular, '['

+          works.

+	}

+

+        \item 'CrlmmSetList': container for results from preprocessing

+	and genotyping.  This object is a list.  The first

+	element of the list is an ABset.  The second element is a

+	SnpSet containing genotype calls.  The two elements are

+	required to have identical featureNames and sampleNames.

+	\enumerate{

+       	  \item added several methods for subsetting and accessing

+ 	  elements of this object, including featureNames,

+ 	  sampleNames, and '['.

+	}

+	

+        \item 'CopyNumberSet': contains locus-level estimates of copy

+  	number for SNPs and polymorphic probes.

+	\enumerate{

+	  \item Required assay data elements are 'CA' and 'CB',

+          corresponding to the absolute copy number for allele

+          A and B, respectively.

+

+	  \item For nonpolymorphic probes, the total copy number is

+          stored in the 'CA' slot and a NA is recorded for the

+          corresponding row in the CB matrix. 

+

+	  \item Useful methods: 'copyNumber', 'ellipse', 'points'

+	}

+      }

+      \item 'crlmmWrapper' function does preprocessing

+      (quantile-normalization) and genotyping, saving an object of

+      class CrlmmSetList for each chromosome

+

+     \item 'computeCopynumber' now requires an object of class

+     'CrlmmSetList' and returns an object of class 'CopyNumberSet'.

+    }

+  }

+}