[med-svn] [r-bioc-limma] 01/03: Imported Upstream version 3.16.18~dfsg

[Charles Plessy]

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plessy pushed a commit to branch master
in repository r-bioc-limma.

commit ff596bedb54da0272f6616d405dc269782746343
Author: Charles Plessy <plessy at debian.org>
Date:   Tue Oct 8 09:41:53 2013 +0900

    Imported Upstream version 3.16.18~dfsg
---
 DESCRIPTION            |    6 +++---
 R/geneset-roast.R      |    4 ++--
 inst/doc/changelog.txt |    4 ++++
 inst/doc/limma.pdf     |  Bin 45597 -> 45597 bytes
 4 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 3cf5b6e..9dd2969 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: limma
-Version: 3.16.7
-Date: 2013/07/29
+Version: 3.16.8
+Date: 2013/09/19
 Title: Linear Models for Microarray Data
 Author: Gordon Smyth with contributions from Matthew Ritchie, Jeremy Silver, James Wettenhall, Natalie Thorne, Mette Langaas, Egil Ferkingstad, Marcus Davy, Francois Pepin, Dongseok Choi, Davis McCarthy, Di Wu, Alicia Oshlack, Carolyn de Graaf, Yifang Hu, Wei Shi and Belinda Phipson.
 Maintainer: Gordon Smyth <smyth at wehi.edu.au>
@@ -14,4 +14,4 @@ URL: http://bioinf.wehi.edu.au/limma
 biocViews: Microarray, OneChannel, TwoChannel, DataImport,
         QualityControl, Preprocessing, Bioinformatics,
         DifferentialExpression, MultipleComparisons, TimeCourse
-Packaged: 2013-07-30 04:07:48 UTC; biocbuild
+Packaged: 2013-09-19 04:07:58 UTC; biocbuild
diff --git a/R/geneset-roast.R b/R/geneset-roast.R
index a8eea42..0445ba2 100644
--- a/R/geneset-roast.R
+++ b/R/geneset-roast.R
@@ -326,7 +326,7 @@ mroast.MAList <- function(y,index=NULL,design=NULL,contrast=ncol(design),set.sta
 mroast.default <- function(y,index=NULL,design=NULL,contrast=ncol(design),set.statistic="mean",gene.weights=NULL,array.weights=NULL,weights=NULL,block=NULL,correlation,var.prior=NULL,df.prior=NULL,trend.var=FALSE,nrot=999,adjust.method="BH",midp=TRUE,sort="directional")
 #  Rotation gene set testing with multiple sets
 #  Gordon Smyth and Di Wu
-#  Created 28 Jan 2010. Last revised 8 Feb 2012.
+#  Created 28 Jan 2010. Last revised 19 Sep 2013.
 {
 #	Check y
 	y <- as.matrix(y)
@@ -375,7 +375,7 @@ mroast.default <- function(y,index=NULL,design=NULL,contrast=ncol(design),set.st
 	NGenes <- rep(0,nsets)
 	if(nsets<1) return(pv)
 	for(i in 1:nsets) {
-		out <- roast(y=y,index=index[[i]],design=design,contrast=contrast,set.statistic=set.statistic,gene.weights=gene.weights,array.weights=array.weights,block=block,correlation=correlation,var.prior=var.prior,df.prior=df.prior,nrot=nrot)
+		out <- roast(y=y,index=index[[i]],design=design,contrast=contrast,set.statistic=set.statistic,gene.weights=gene.weights,array.weights=array.weights,weights=weights,block=block,correlation=correlation,var.prior=var.prior,df.prior=df.prior,nrot=nrot)
 		pv[i,] <- out$p.value$P.Value
 		active[i,] <- out$p.value$Active.Prop
 		NGenes[i] <- out$ngenes.in.set
diff --git a/inst/doc/changelog.txt b/inst/doc/changelog.txt
index 47492d7..a5f23de 100755
--- a/inst/doc/changelog.txt
+++ b/inst/doc/changelog.txt
@@ -1,3 +1,7 @@
+19 September 2013: limma 3.16.8
+
+- bug fix to mroast() which was not using weights correctly.
+
 29 July 2013: limma 3.16.7
 
 - duplicateCorrelation() now uses the weights matrix when block is
diff --git a/inst/doc/limma.pdf b/inst/doc/limma.pdf
index af98632..a53a2ad 100644
Binary files a/inst/doc/limma.pdf and b/inst/doc/limma.pdf differ

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