[med-svn] [r-bioc-limma] 01/03: New upstream version 3.30.7+dfsg

[Andreas Tille]

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

commit c1af0b7cad088870803c795dd1758789293657b7
Author: Andreas Tille <tille at debian.org>
Date:   Thu Jan 5 15:31:42 2017 +0100

    New upstream version 3.30.7+dfsg
---
 DESCRIPTION            |   6 +++---
 R/contrastAsCoef.R     |  17 +++++++++--------
 inst/doc/changelog.txt |   6 ++++++
 inst/doc/intro.pdf     | Bin 43301 -> 43301 bytes
 4 files changed, 18 insertions(+), 11 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 195d092..f017186 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: limma
-Version: 3.30.6
-Date: 2016-11-28
+Version: 3.30.7
+Date: 2016-12-14
 Title: Linear Models for Microarray Data
 Description: Data analysis, linear models and differential expression for microarray data.
 Author: Gordon Smyth [cre,aut], Yifang Hu [ctb], Matthew Ritchie [ctb], Jeremy Silver [ctb], James Wettenhall [ctb], Davis McCarthy [ctb], Di Wu [ctb], Wei Shi [ctb], Belinda Phipson [ctb], Aaron Lun [ctb], Natalie Thorne [ctb], Alicia Oshlack [ctb], Carolyn de Graaf [ctb], Yunshun Chen [ctb], Mette Langaas [ctb], Egil Ferkingstad [ctb], Marcus Davy [ctb], Francois Pepin [ctb], Dongseok Choi [ctb]
@@ -21,4 +21,4 @@ biocViews: ExonArray, GeneExpression, Transcription,
         MultipleComparison, Normalization, Preprocessing,
         QualityControl
 NeedsCompilation: yes
-Packaged: 2016-11-28 23:13:27 UTC; biocbuild
+Packaged: 2016-12-14 23:12:22 UTC; biocbuild
diff --git a/R/contrastAsCoef.R b/R/contrastAsCoef.R
index efa3dbc..b0b87e0 100644
--- a/R/contrastAsCoef.R
+++ b/R/contrastAsCoef.R
@@ -1,26 +1,27 @@
 contrastAsCoef <- function(design, contrast=NULL, first=TRUE)
 #	Reform a design matrix so that one or more contrasts become simple coefficients
 #	Gordon Smyth
-#	31 August 2013
+#	31 August 2013. Last modified 14 Dec 2016.
 {
 	design <- as.matrix(design)
 	if(is.null(contrast)) return(design)
 	contrast <- as.matrix(contrast)
 	if(ncol(design) != nrow(contrast)) stop("Length of contrast doesn't match ncol(design)")
-	qrc <- qr(contrast)
-	ncontrasts <- qrc$rank
+	QRc <- qr(contrast)
+	ncontrasts <- QRc$rank
 	if(ncontrasts==0) stop("contrast is all zero")
 	coef <- 1:ncontrasts
-	Dvec <- diag(qrc$qr)[coef]
-	design <- t(qr.qty(qrc,t(design)))
+	designT <- qr.qty(QRc,t(design))
+	R <- QRc$qr[coef,]
+	designT[coef,] <- backsolve(R,designT[coef,,drop=FALSE])
+	design <- t(designT)
 	colnames(design) <- paste("Q",1:ncol(design),sep="")
 	cn <- colnames(contrast)
-	if(is.null(cn)) cn <- paste("C",qrc$pivot[coef],sep="")
+	if(is.null(cn)) cn <- paste("C",QRc$pivot[coef],sep="")
 	colnames(design)[coef] <- cn
 	if(!first) {
 		design <- cbind(design[,-coef,drop=FALSE],design[,coef,drop=FALSE])
 		coef <- rev( ncol(design)-coef+1 )
 	}
-	design[,coef] <- t(t(design[,coef])/Dvec)
-	list(design=design,coef=coef,qr=qrc)
+	list(design=design,coef=coef,qr=QRc)
 }
diff --git a/inst/doc/changelog.txt b/inst/doc/changelog.txt
index 7d774fa..df5ccb6 100755
--- a/inst/doc/changelog.txt
+++ b/inst/doc/changelog.txt
@@ -1,3 +1,9 @@
+14 Dec 2016: limma 3.30.7
+
+- Bug fix for contrastAsCoef() when there is more than one contrast.
+  Previously the coefficients for the transformed design matrix were
+  correct only for the first contrast.
+
 28 Nov 2016: limma 3.30.6
 
 - plotSA() now indicates, by way of an open plotting symbol, any
diff --git a/inst/doc/intro.pdf b/inst/doc/intro.pdf
index 64e6815..9709c3a 100644
Binary files a/inst/doc/intro.pdf and b/inst/doc/intro.pdf differ

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