@@ -230,6 +230,11 @@ is decoded and scanned

 * added .man page for .computeCopynumber 

-* Suggests VanillaICE (>= 1.7.8)  -- needed to run the copynumber.Rnw vignette

+* Suggests VanillaICE (>= 1.7.8)  -- needed to run the copynumber.Rnw

+  vignette

+

+2009-07-16 R Scharpf - committed version 1.3.13

+

+* fixed bug 'DF.PRIOR not found'

@@ -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: 1.3.12

+Version: 1.3.13

 Date: 2009-06-17

 Author: Rafael A Irizarry, Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>

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

@@ -482,7 +482,7 @@ computeCopynumber <- function(object,

 	##previous version of compute copy number

 	envir <- new.env()

 	message("Fitting model for copy number estimation...")

-	message("Using ", DF.PRIOR, " df for inverse chi squares.")	

+

 	.computeCopynumber(chrom=CHR,

 			   A=A(ABset),

 			   B=B(ABset),

@@ -823,6 +823,7 @@ thresholdCopyNumberSet <- function(object){

 		if(length(plate) != ncol(A))

 			stop("plate must the same length as the number of columns of A")

 	}

+	message("Using ", DF.PRIOR, " df for inverse chi squares.")		

 	set.seed(seed)

 	if(length(ls(envir)) == 0) {

 		instantiateObjects(calls=calls,