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commit c1af0b7cad088870803c795dd1758789293657b7 Author: Andreas Tille <[email protected]> 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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-limma.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
