[med-svn] [r-bioc-edger] 01/03: Imported Upstream version 3.6.8+dfsg

[Andreas Tille]

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in repository r-bioc-edger.

commit 691b0494663e091bb67bc3962e8767093092f850
Author: Andreas Tille <tille at debian.org>
Date:   Thu Sep 18 15:42:16 2014 +0200

    Imported Upstream version 3.6.8+dfsg
---
 DESCRIPTION                 |   6 +++---
 R/readDGE.R                 |   2 +-
 inst/doc/edgeR.pdf          | Bin 48051 -> 48051 bytes
 tests/edgeR-Tests.Rout.save |   2 +-
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 800276a..1060425 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: edgeR
-Version: 3.6.7
-Date: 2014/07/15
+Version: 3.6.8
+Date: 2014/08/14
 Title: Empirical analysis of digital gene expression data in R
 Author: Yunshun Chen <yuchen at wehi.edu.au>, Davis McCarthy <dmccarthy at wehi.edu.au>, Aaron Lun <alun at wehi.edu.au>, Mark Robinson <mark.robinson at imls.uzh.ch>, Xiaobei Zhou <xiaobei.zhou at uzh.ch>, Gordon Smyth <smyth at wehi.edu.au>
 Maintainer: Yunshun Chen <yuchen at wehi.edu.au>, Mark Robinson <mark.robinson at imls.uzh.ch>, Davis McCarthy <dmccarthy at wehi.edu.au>, Gordon Smyth <smyth at wehi.edu.au>
@@ -15,4 +15,4 @@ biocViews: GeneExpression, Transcription, AlternativeSplicing,
         TimeCourse, SAGE, Sequencing, ChIPSeq, RNASeq, BatchEffect,
         MultipleComparison, Normalization, QualityControl
 Description: Differential expression analysis of RNA-seq and digital gene expression profiles with biological replication.  Uses empirical Bayes estimation and exact tests based on the negative binomial distribution.  Also useful for differential signal analysis with other types of genome-scale count data.
-Packaged: 2014-07-16 02:04:59 UTC; biocbuild
+Packaged: 2014-08-15 02:04:09 UTC; biocbuild
diff --git a/R/readDGE.R b/R/readDGE.R
index 5b26cff..67af8c2 100644
--- a/R/readDGE.R
+++ b/R/readDGE.R
@@ -8,7 +8,7 @@ readDGE <- function(files,path=NULL,columns=c(1,2),group=NULL,labels=NULL,...)
 		if(is.null(labels)) labels <- row.names(files)
 		files <- files$files
 	} else {
-		x$samples <- data.frame(files=as.character(files),stringsAsFactors=FALSE)
+		x$samples <- data.frame(files=as.character(files),group=1,stringsAsFactors=FALSE)
 	}
 	if(!is.null(group)) x$samples$group <- group
 	if(!is.null(x$samples$group)) x$samples$group <- as.factor(x$samples$group)
diff --git a/inst/doc/edgeR.pdf b/inst/doc/edgeR.pdf
index 7c5c896..607b303 100644
Binary files a/inst/doc/edgeR.pdf and b/inst/doc/edgeR.pdf differ
diff --git a/tests/edgeR-Tests.Rout.save b/tests/edgeR-Tests.Rout.save
index 07a738b..8fc2197 100644
--- a/tests/edgeR-Tests.Rout.save
+++ b/tests/edgeR-Tests.Rout.save
@@ -422,7 +422,7 @@ $n0
 > proc.time()
    user  system elapsed 
    3.41    0.03    3.44 
-                                                                                                                                                                                                                                                                      edgeR/vignettes/                                                                                    0000755 0001263 0001264 00000000000 12361356713 015202  5                                                                          [...]
+                                                                                                                                                                                                                                                                      edgeR/vignettes/                                                                                    0000755 0001263 0001264 00000000000 12373265231 015177  5                                                                          [...]
 %\VignetteKeyword{RNA-Seq}
 %\VignetteKeyword{differential expression}
 %\VignettePackage{edgeR}

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