@@ -1,6 +1,6 @@

 Package: GSVA

-Version: 1.7.4

-Date: 2013-1-7

+Version: 1.7.5

+Date: 2013-1-16

 Title: Gene Set Variation Analysis for microarray and RNA-seq data

 Author: Justin Guinney <justin.guinney@sagebase.org> (with contributions from Robert Castelo <robert.castelo@upf.edu> and Sonja Haenzelmann <shanzelmann@imim.es)

 Maintainer: Justin Guinney <justin.guinney@sagebase.org>

@@ -13,4 +13,4 @@ License: GPL (>= 2)

 LazyLoad: yes

 biocViews: Microarray, Pathways, GeneSetEnrichment

 URL: http://www.sagebase.org

-

+Encoding: latin1

@@ -23,6 +23,17 @@ setMethod("gsva", signature(expr="ExpressionSet", gset.idx.list="list", annotati

 {

   method <- match.arg(method)

+  ## filter out genes with constant expression values

+  sdGenes <- Biobase::esApply(expr, 1, sd)

+  if (any(sdGenes == 0)) {

+    if (verbose)

+      cat("Filtering out ", sum(sdGenes), " genes with constant expression values throuhgout the samples\n")

+    expr <- expr[sdGenes > 0, ]

+  } 

+

+  if (nrow(expr) < 2)

+    stop("Less than two genes in the input ExpressionSet object\n")

+

   ## map to the actual features for which expression data is available

   mapped.gset.idx.list <- lapply(gset.idx.list,

                                  function(x, y) na.omit(match(x, y)),

@@ -66,6 +77,17 @@ setMethod("gsva", signature(expr="ExpressionSet", gset.idx.list="GeneSetCollecti

 {

   method <- match.arg(method)

+  ## filter out genes with constant expression values

+  sdGenes <- Biobase::esApply(expr, 1, sd)

+  if (any(sdGenes == 0)) {

+    if (verbose)

+      cat("Filtering out ", sum(sdGenes), " genes with constant expression values throuhgout the samples\n")

+    expr <- expr[sdGenes > 0, ]

+  } 

+

+  if (nrow(expr) < 2)

+    stop("Less than two genes in the input ExpressionSet object\n")

+

   if (verbose)

     cat("Mapping identifiers between gene sets and feature names\n")

@@ -116,6 +138,17 @@ setMethod("gsva", signature(expr="matrix", gset.idx.list="GeneSetCollection", an

 {

   method <- match.arg(method)

+  ## filter out genes with constant expression values

+  sdGenes <- apply(expr, 1, sd)

+  if (any(sdGenes == 0)) {

+    if (verbose)

+      cat("Filtering out ", sum(sdGenes), " genes with constant expression values throuhgout the samples\n")

+    expr <- expr[sdGenes > 0, ]

+  } 

+

+  if (nrow(expr) < 2)

+    stop("Less than two genes in the input expression data matrix\n")

+

   ## map gene identifiers of the gene sets to the features in the matrix

   mapped.gset.idx.list <- gset.idx.list

   if (!is.na(annotation)) {

@@ -123,7 +156,7 @@ setMethod("gsva", signature(expr="matrix", gset.idx.list="GeneSetCollection", an

       cat("Mapping identifiers between gene sets and feature names\n")

     mapped.gset.idx.list <- GSEABase::mapIdentifiers(gset.idx.list,

-                                                     GSEABase::AnnoOrEntrezIdentifier(Biobase::annotation))

+                                                     GSEABase::AnnoOrEntrezIdentifier(annotation))

   }

   ## map to the actual features for which expression data is available

@@ -161,6 +194,17 @@ setMethod("gsva", signature(expr="matrix", gset.idx.list="list", annotation="mis

 {

   method <- match.arg(method)

+  ## filter out genes with constant expression values

+  sdGenes <- apply(expr, 1, sd)

+  if (any(sdGenes == 0)) {

+    if (verbose)

+      cat("Filtering out ", sum(sdGenes), " genes with constant expression values throuhgout the samples\n")

+    expr <- expr[sdGenes > 0, ]

+  } 

+

+  if (nrow(expr) < 2)

+    stop("Less than two genes in the input expression data matrix\n")

+

   mapped.gset.idx.list <- lapply(gset.idx.list,

                                  function(x ,y) na.omit(match(x, y)),

                                  rownames(expr))

@@ -1,13 +1,17 @@

 citHeader("To cite package 'GSVA' in publications use:")

 citEntry(entry="Article",

-  author = personList(as.person("Sonja H\"anzelmann"),

+  title = "{GSVA}: gene set variation analysis for microarray and {RNA-Seq} data",

+  author = personList(as.person("Sonja H{\\\"a}nzelmann"),

                       as.person("Robert Castelo"),

                       as.person("Justin Guinney")),

-  title = "GSVA: Gene Set Variation Analysis for microarray and RNA-Seq data",

-  journal = "BMC Bioinformatics, in press",

+  journal = "BMC Bioinformatics",

+  volume = "14",

+  pages = "7",

   year = "2013",

-  textVersion = paste("Hanzelmann, S., Castelo, R. and Guinney, A.",

-                      "GSVA: Gene Set Variation Analysis for microarray and RNA-seq data",

-                      "BMC Bioinformatics, in press, 2013.")

+  url = "http://www.biomedcentral.com/1471-2105/14/7",

+  doi = "10.1186/1471-2105-14-7",

+  textVersion = paste("H�nzelmann, S., Castelo, R. and Guinney, A.",

+                      "GSVA: gene set variation analysis for microarray and RNA-seq data.",

+                      "BMC Bioinformatics, 14:7, 2013.")

 )

@@ -5,6 +5,8 @@

 \alias{computeGeneSetsOverlap,GeneSetCollection,character-method}

 \alias{computeGeneSetsOverlap,GeneSetCollection,ExpressionSet-method}

+\encoding{latin1}

+

 \title{

 Compute gene-sets overlap

 }

@@ -38,8 +40,9 @@ size of the two gene sets.

 A gene-set by gene-set matrix of the overlap among every pair of gene sets.

 }

 \references{

-H\"anzelmann, S., Castelo, R. and Guinney, J.

-GSVA: Gene Set Variation Analysis for microarray and RNA-Seq data, \emph{BMC Bioinformatics, in press, 2013.}

+\enc{H�nzelmann}{Hanzelmann}, S., Castelo, R. and Guinney, J.

+GSVA: Gene set variation analysis for microarray and RNA-Seq data.

+\emph{BMC Bioinformatics}, 14:7, 2013.

 }

 \author{J. Guinney}

 \seealso{

@@ -3,6 +3,8 @@

 \alias{filterGeneSets,list-method}

 \alias{filterGeneSets,GeneSetCollection-method}

+\encoding{latin1}

+

 \title{

 Filter gene sets

 }

@@ -26,8 +28,9 @@ This function filters the input gene sets according to a given minimum and maxim

 A collection of gene sets that meet the given minimum and maximum set size.

 }

 \references{

-H\"anzelmann, S., Castelo, R. and Guinney, J.

-GSVA: Gene Set Variation Analysis for microarray and RNA-Seq data, \emph{BMC Bioinformatics, in press, 2013.}

+\enc{H�nzelmann}{Hanzelmann}, S., Castelo, R. and Guinney, J.

+GSVA: Gene set variation analysis for microarray and RNA-Seq data.

+\emph{BMC Bioinformatics}, 14:7, 2013.

 }

 \author{J. Guinney}

 \seealso{

@@ -5,6 +5,8 @@

 \alias{gsva,matrix,GeneSetCollection,character-method}

 \alias{gsva,matrix,list,missing-method}

+\encoding{latin1}

+

 \title{

 Gene Set Variation Analysis

 }

@@ -146,8 +148,9 @@ A gene-set by sample matrix of GSVA enrichment scores.

 Barbie, D.A. et al. Systematic RNA interference reveals that oncogenic KRAS-driven

 cancers require TBK1. \emph{Nature}, 462(5):108-112, 2009.

-H\"anzelmann, S., Castelo, R. and Guinney, J.

-GSVA: Gene Set Variation Analysis for microarray and RNA-Seq data, \emph{BMC Bioinformatics, in press, 2013.}

+\enc{H�nzelmann}{Hanzelmann}, S., Castelo, R. and Guinney, J.

+GSVA: Gene set variation analysis for microarray and RNA-Seq data.

+\emph{BMC Bioinformatics}, 14:7, 2013.

 Lee, E. et al. Inferring pathway activity toward precise disease classification.

 \emph{PLoS Comp Biol}, 4(11):e1000217, 2008.