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

 Package: GSVA

-Version: 1.11.2

-Date: 2013-10-21

+Version: 1.11.3

+Date: 2014-01-13

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

 Author: Justin Guinney with contributions from Robert Castelo

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

@@ -1,6 +1,8 @@

 useDynLib(GSVA)

 import(methods)

+import(BiocGenerics)

+

 importClassesFrom(Biobase, ExpressionSet)

 importClassesFrom(GSEABase, GeneSetCollection)

 importFrom(Biobase, exprs)

@@ -45,14 +45,11 @@ setMethod("gsva", signature(expr="ExpressionSet", gset.idx.list="list", annotati

                                          min.sz=max(1, min.sz),

                                          max.sz=max.sz)

-  eSco <- GSVA:::.gsva(Biobase::exprs(expr), mapped.gset.idx.list, method, rnaseq, abs.ranking,

+  eSco <- GSVA:::.gsva(exprs(expr), mapped.gset.idx.list, method, rnaseq, abs.ranking,

                        no.bootstraps, bootstrap.percent, parallel.sz, parallel.type,

                        mx.diff, tau, kernel, verbose)

-  eScoEset <- expr

-  ## eScoEset <- Biobase::`exprs<-`(eScoEset, eSco$es.obs)

-  ## eScoEset <- Biobase::`annotation<-`(eScoEset, value="")

-  Biobase::exprs(eScoEset) <- eSco$es.obs

-  Biobase::annotation(eScoEset) <- ""

+  eScoEset <- new("ExpressionSet", exprs=eSco$es.obs, phenoData=phenoData(expr),

+                  experimentData=experimentData(expr), annotation="")

 	return(list(es.obs=eScoEset,

 				      bootstrap=eSco$bootstrap,

@@ -93,7 +90,7 @@ setMethod("gsva", signature(expr="ExpressionSet", gset.idx.list="GeneSetCollecti

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

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

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

+                                                   GSEABase::AnnoOrEntrezIdentifier(annotation(expr)))

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

   tmp <- lapply(geneIds(mapped.gset.idx.list),

@@ -106,14 +103,11 @@ setMethod("gsva", signature(expr="ExpressionSet", gset.idx.list="GeneSetCollecti

                                          min.sz=max(1, min.sz),

                                          max.sz=max.sz)

-  eSco <- GSVA:::.gsva(Biobase::exprs(expr), mapped.gset.idx.list, method, rnaseq, abs.ranking,

+  eSco <- GSVA:::.gsva(exprs(expr), mapped.gset.idx.list, method, rnaseq, abs.ranking,

                        no.bootstraps, bootstrap.percent, parallel.sz, parallel.type,

                        mx.diff, tau, kernel, verbose)

-  eScoEset <- expr

-  ## eScoEset <- Biobase::`exprs<-`(eScoEset, eSco$es.obs)

-  ## eScoEset <- Biobase::`annotation<-`(eScoEset, value="")

-  Biobase::exprs(eScoEset) <- eSco$es.obs

-  Biobase::annotation(eScoEset) <- ""

+  eScoEset <- new("ExpressionSet", exprs=eSco$es.obs, phenoData=phenoData(expr),

+                  experimentData=experimentData(expr), annotation="")

 	return(list(es.obs=eScoEset,

 				      bootstrap=eSco$bootstrap,

@@ -949,7 +943,7 @@ setMethod("computeGeneSetsOverlap", signature(gSets="GeneSetCollection", uniqGen

 setMethod("computeGeneSetsOverlap", signature(gSets="GeneSetCollection", uniqGenes="ExpressionSet"),

           function(gSets, uniqGenes, min.sz=1, max.sz=Inf) {

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

-  gSets <- GSEABase::mapIdentifiers(gSets, GSEABase::AnnoOrEntrezIdentifier(Biobase::annotation(uniqGenes)))

+  gSets <- GSEABase::mapIdentifiers(gSets, GSEABase::AnnoOrEntrezIdentifier(annotation(uniqGenes)))

   uniqGenes <- Biobase::featureNames(uniqGenes)