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

 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: 1.11.0

+Version: 1.11.1

 Date: 2010-12-10

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

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

@@ -100,6 +100,7 @@ construct <- function(filenames,

 }

 constructAffy <- function(filenames, sns, cdfName, batch, verbose=TRUE){

+	stopifnot(length(sns)==length(batch))

 	is.lds <- ifelse(isPackageLoaded("ff"), TRUE, FALSE)

 	if(!is.lds) stop("this function now requires that the ff package be loaded")

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

@@ -21,12 +21,20 @@

 \section{Methods}{

   \describe{

-    \item{Ns}{\code{signature(object="AssayData")}: ...}

-    \item{corr}{\code{signature(object="AssayData")}: ...}

-    \item{mads}{\code{signature(x="AssayData")}: ...}

-    \item{medians}{\code{signature(object="AssayData")}: ...}

-    \item{tau2}{\code{signature(object="AssayData")}: ...}

-	 }

+    \item{Ns}{\code{signature(object="AssayData")}:  Accessor for genotype

+  frequencies}

+    \item{corr}{\code{signature(object="AssayData")}: Accessor for the correlation of the

+  log-transformed normalized intensities within the diallelic genotype clusters}

+    \item{mads}{\code{signature(x="AssayData")}: Accessor for the median

+  absolute deviation of the  normalized intensities within the

+  diallelic genotype clusters }

+    \item{medians}{\code{signature(object="AssayData")}: Accessor for

+  the posterior mean of the normalized intensity within the diallelic genotype

+  clusters.}

+    \item{tau2}{\code{signature(object="AssayData")}: Accessor for the

+  median absolute deviation of the log-transformed intensities within

+  the diallelic genotype clusters}

+  }

 }

 \seealso{

@@ -33,17 +33,24 @@

 \section{Methods}{

   \describe{

-    \item{CA}{\code{signature(object="CNSet")}: ...}

-    \item{CB}{\code{signature(object="CNSet")}: ...}

-    \item{lines}{\code{signature(x="CNSet")}: ...}

-    \item{totalCopynumber}{\code{signature(object="CNSet")}: ...}

-    \item{rawCopynumber}{\code{signature(object="CNSet")}: ...}

-    \item{nuA}{\code{signature(object="CNSet")}: ...}

-    \item{nuB}{\code{signature(object="CNSet")}: ...}

-    \item{phiA}{\code{signature(object="CNSet")}: ...}

-    \item{phiB}{\code{signature(object="CNSet")}: ...}

-    \item{Ns}{\code{signature(object="CNSet")}: ...}

-    \item{corr}{\code{signature(object="CNSet")}: ...}

+    \item{CA}{\code{signature(object="CNSet")}: calculates raw copy number

+  for allele A}

+    \item{CB}{\code{signature(object="CNSet")}: calculates raw copy

+  number for allele B}

+    \item{lines}{\code{signature(x="CNSet")}: plot ellipses (95th

+  percentile) for prediction regions}

+    \item{totalCopynumber}{\code{signature(object="CNSet")}: calculates

+  total raw copy number}

+    \item{rawCopynumber}{\code{signature(object="CNSet")}: same as totalCopynumber}

+    \item{nuA}{\code{signature(object="CNSet")}: estimate of mean

+  background (intensity-scale) for allele A}

+    \item{nuB}{\code{signature(object="CNSet")}: estimate of mean

+  background (intensity-scale) for allele A}

+    \item{phiA}{\code{signature(object="CNSet")}: estimate of slope coefficient (intensity-scale) for allele A}

+    \item{phiB}{\code{signature(object="CNSet")}: estimate of slope coefficient (intensity-scale) for allele B}

+    \item{Ns}{\code{signature(object="CNSet")}: genotype frequencies }

+    \item{corr}{\code{signature(object="CNSet")}: correlation of

+  log-transformed normalized intensities within the genotype clusters}

     \item{mads}{\code{signature(x="CNSet")}: ...}

     \item{medians}{\code{signature(object="CNSet")}: ...}

     \item{tau2}{\code{signature(object="CNSet")}: ...}