[med-svn] [r-bioc-limma] 01/01: Imported Upstream version 3.18.1~dfsg
Charles Plessy
plessy at alioth.debian.org
Thu Oct 31 01:12:25 UTC 2013
This is an automated email from the git hooks/post-receive script.
plessy pushed a commit to branch upstream
in repository r-bioc-limma.
commit eab8baa83416641df73d5e6dd04b6be2b077bbf1
Author: Charles Plessy <plessy at debian.org>
Date: Thu Oct 31 10:08:48 2013 +0900
Imported Upstream version 3.18.1~dfsg
---
DESCRIPTION | 6 +-
inst/NEWS.Rd | 146 +++++++++++++++++++++++++++++++++++++++++++++---
inst/doc/changelog.txt | 8 ++-
inst/doc/limma.pdf | Bin 45597 -> 45597 bytes
4 files changed, 149 insertions(+), 11 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 6bfd4f1..4441e3f 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: limma
-Version: 3.18.0
-Date: 2013/10/11
+Version: 3.18.1
+Date: 2013/10/23
Title: Linear Models for Microarray Data
Author: Gordon Smyth [cre,aut], Matthew Ritchie [ctb], Jeremy Silver [ctb], James Wettenhall [ctb], Natalie Thorne [ctb], Mette Langaas [ctb], Egil Ferkingstad [ctb], Marcus Davy [ctb], Francois Pepin [ctb], Dongseok Choi [ctb], Davis McCarthy [ctb], Di Wu [ctb], Alicia Oshlack [ctb], Carolyn de Graaf [ctb], Yifang Hu [ctb], Wei Shi [ctb], Belinda Phipson [ctb]
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: 2013-10-15 03:16:09 UTC; biocbuild
+Packaged: 2013-10-24 03:20:08 UTC; biocbuild
diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
index b4fd7a6..45eabec 100644
--- a/inst/NEWS.Rd
+++ b/inst/NEWS.Rd
@@ -2,6 +2,138 @@
\title{limma News}
\encoding{UTF-8}
+\section{Version 3.18.0}{\itemize{
+
+\item
+new function beadCountWeights() to estimate quantitative weights
+from the bead counts for each probe for Illumina BeadArrays.
+
+\item
+New function contrastAsCoef(), which reforms a design matrix so
+that one or more specified contrasts become coefficients. This
+function is called by roast().
+
+\item
+plotMA() is now an S3 generic function.
+
+\item
+The legend argument to plotMA() can now take a character value
+giving the position to place the legend.
+
+\item
+toptable(), topTable() and topTreat() now preserve the rownames of
+the fit object, unless the fit object has duplicated names, in
+which case the rownames are copied to the ID column. Empty
+rownames are replaced with 1:nrow(fit).
+
+\item
+read.ilmn() no longer adds the probe IDs to the gene annotation
+data.frame, leaving them instead as rownames of the expression
+matrix. It longer creates a targets file since the sample names
+are already preserved as column names of the expression matrix.
+
+\item
+loessFit() now uses the locfit.raw in the locfit package when
+weights are provided instead of loess in the stats package. The
+function now runs very efficiently even on very long data vectors.
+The output results will change slightly when weights are provided.
+
+\item
+voom() now outputs lib.size as a column of targets instead of as a
+separate component.
+
+\item
+cbind for EList and EListRaw objects now recognizes a design matrix
+if it is present.
+
+\item
+plotMDS() now checks explicitly that there are at least 3 samples
+to plot.
+
+\item
+normexp.fit.detection.p() now tolerates some non-monotonicity in
+the detection p-pvalues as a function of expression.
+
+\item
+fitFDistRobustly() now uses a smoother for the smallest df.prior
+values. This may result in smaller tail values than before when
+a group of input x values appear to be outliers but the largest
+value is not individually a stand-out value.
+
+\item
+New merge methods for EList and EListRaw objects.
+
+\item
+topTable() and treat() now give more informative error messages
+when the argument fit is not a valid MArrayLM object.
+
+\item
+roast() now calls mroast() if the index vector is a list.
+Bug fix to mroast(), which had been ignoring the weights.
+
+\item
+Updates to genas() function.
+argument chooseMethod renamed to subset and option "n" renamed to "all".
+Function now returns NA results and a message when no genes satisfy
+the criterion for inclusion in the analysis.
+Some editing of help page and streamlining of code.
+
+\item
+Roles of contributors now specified in author field of DESCRIPTION
+file using standard codes.
+
+\item
+Additions and updates to references in the help pages.
+Removed defunct Berkeley Press links to published Smyth (2004)
+article in several Rd files. Replacing with link to Preprint.
+Added link to Phipson (2013) thesis in two Rd files.
+Add Majewski et al reference to genas.Rd.
+Add Phipson et al and Sartor et al references to squeezeVar.Rd.
+Add Phipson et al reference to eBayes.Rd.
+Update lmscFit and voom references.
+
+\item
+Update mammmary stem cell case study in User's Guide. As well
+as reflecting changes to read.ilmn() and topTable(), this now
+demonstrates how to find signature genes for particular cell type.
+
+\item
+documentation about rownames and column names and the use of
+rownames(fit) and colnames(fit) added to lmFit.Rd.
+
+\item
+improvements to help pages for data classes.
+
+\item
+Edits to normalizeBetweenArrays help page (i) to further clarify
+which normalization methods are available for single-channel data
+and which are available for two-color data and (ii) to give a cross
+citation to the neqc() function for Illumina BeadChips.
+
+\item
+Edits to voomaByGroup help page.
+
+\item
+duplicateCorrelation() now uses the weights matrix when block is
+set. Previously the weights were ignored when block was used.
+
+\item
+Bug fix to subsetting for MArrayLM objects: the df.total component
+was not being subsetted.
+
+\item
+bug fix to eBayes(robust=TRUE) when some of the df.prior values are
+infinite.
+
+\item
+Bug fix to ebayes(), which was not passing the 'robust' argument
+correctly on to squeezeVar().
+
+\item
+Bug fix to fitFDistRobustly(), which affected the estimated scale
+when df2 is estimated to be Inf.
+}}
+
\section{Version 3.16.0}{\itemize{
@@ -15,16 +147,16 @@ Previously the meaning of source="agilent" was mis-stated in read.maimages.Rd.
\item
New robust method for estimating the empirical Bayes prior, called
- by specifying robust=TRUE in the call to eBayes(). When this is
- TRUE the output df.prior is now a vector instead of a scalar.
+by specifying robust=TRUE in the call to eBayes(). When this is
+TRUE the output df.prior is now a vector instead of a scalar.
\item
New function fitFDistRobustly() estimates the parameters of a
- scaled F-distribution robustly using Winsorized values. Outlier
- observations receive smaller values for df.prior than non-outliers.
- This permits robust methods for squeezeVar(), ebayes() and eBayes(),
- all of which now have a new argument wins.tail.p to specify the
- tail proportions for Winsorizing.
+scaled F-distribution robustly using Winsorized values. Outlier
+observations receive smaller values for df.prior than non-outliers.
+This permits robust methods for squeezeVar(), ebayes() and eBayes(),
+all of which now have a new argument wins.tail.p to specify the
+tail proportions for Winsorizing.
\item
fitFDist() now permits infinite values for the covariate.
diff --git a/inst/doc/changelog.txt b/inst/doc/changelog.txt
index 5fbadff..f5f1e49 100755
--- a/inst/doc/changelog.txt
+++ b/inst/doc/changelog.txt
@@ -1,3 +1,9 @@
+23 Oct 2013: limma 3.18.1
+
+- NEWS.Rd updated to reflect changes in Bioconductor 2.13 Release.
+
+15 Oct 2013: limma 3.18.0 (Bioconductor 2.13 Release Branch)
+
11 Oct 2013: limma 3.17.28
- Add comment to RNA-seq case study in User's Guide about conflict
@@ -109,7 +115,7 @@
- Update lmscFit and voom references.
-- Update voomByGroup documentation.
+- Update voomaByGroup documentation.
12 May 2013: limma 3.17.12
diff --git a/inst/doc/limma.pdf b/inst/doc/limma.pdf
index 5d8cf4a..1c12e39 100644
Binary files a/inst/doc/limma.pdf and b/inst/doc/limma.pdf differ
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